Thank you, this is nice and easy to read.

Thank you, this is nice and easy to read.

Unless the clans are in open warfare or close to it, I have rarely had problems with mixed clan groups. The clans often have alliances, marriages, students in each other's dojos, hostages and other such connections between them.
Unless your group only does what some superior NPC tells them to, interwoven Giri and Ninjo will make them work together regardless of clan allegiances.

Unless the clans are in open warfare or close to it, I have rarely had problems with mixed clan groups. The clans often have alliances, marriages, students in each other's dojos, hostages and other such connections between them.
Unless your group only does what some superior NPC tells them to, interwoven Giri and Ninjo will make them work together regardless of clan allegiances.

For Sensei title ability I would use Venerable Provincial Daimyo's Lord's Command (Core book page 315): Once per scene as Support, sensei may advise single character in action and the target may use sensei's Ring or Skill rating instead on next roll to perform the action.

In addition, Courts of Stone has Castellan title, which is second only to Daimyo in authority in the domain.

In addition, Courts of Stone has Castellan title, which is second only to Daimyo in authority in the domain.

I like 5e, but as others have noted, FFG has removed a lot of the bite from the Shadowlands Taint. I'd like to try out some homebrew rules that make it something a little closer to what it was in previous editions. Here are some thoughts I just cobbled together. Let me know what you think.
Shadowlands Taint
This becomes a 0-100 scale, like Glory, Honor, and Status. You gain a Shadowlands Taint disadvantage at 10 and another every 20 points beyond it (30, 50, 70, and 90). I'm not sure yet at what point a character becomes too tainted to be playable; I'm likely to leave that to GM discretion.
Shadowlands Taint Resist checks
Every two weeks, a character with 1 or more Shadowlands Taint points must make a TN 4 Fitness or Meditation check. They can use any ring for the check, as long as they don't have a Shadowlands Taint disadvantage associated with the ring. If they pass, they stave off the corrupting influence of the Shadowlands for a little longer. If they fail, they gain a number of Shadowlands Taint points equal to four times their shortfall. If this increase in points causes them to gain a new Shadowlands Taint disadvantage, it must be in the ring they used for the check.
Afflicted
Scratch the last paragraph of the Afflicted entry (about making a check or getting the Shadowlands Taint disadvantage). Add the following to the Effects section:
An Afflicted character must make Shadowlands Taint Resist checks as though they had Shadowlands Taint points, even if they have none.
Time Spent in the Shadowlands
At the end of each day spent in the Shadowlands, a player must roll a Fitness or Meditation check to resist acquiring Shadowlands Taint. They can use any ring for the check, as long as they don't have a Shadowlands Taint disadvantage associated with the ring. On the first day, the TN is 1. Increase the TN by 1 if they have an open wound (by GM discretion, but a good starting point is a wound from the last 24 hours that caused the Bleeding, Unconscious, or Severely Wounded conditions). Increase the TN by 1 if they have the Afflicted condition. If they pass, increase the TN by 1 for the next check to resist the Shadowlands Taint in this way. For every two bonus successes, they can go one day without needing to make a check. If they fail, they gain a number of Taint points equal to four times their shortfall (but the TN for the next check is not increased).
Example: Hiruma Do is scouting in the Shadowlands. At the end of the first day, he rolls to resist the Shadowlands Taint. Because it’s only been one day, the TN is 1. He gets three successes. Having two bonus successes means he doesn’t need to roll at the end of the second day. On the third day, he’ll roll against a TN of 2. If on the third day he had an open wound or was Afflicted, the TN would be 3. If he had an open wound and was Afflicted, the TN would be 4.
Maho
Every time a character performs a Maho technique, they gain Shadowlands Taint points equal to four times the rank of the technique plus the number of strife kept. These Taint points are acquired, even if the Maho fails. Every Maho technique also gains the following new opportunity:
[opp+]: Reduce the number of Taint points gained from using this technique by the number of opportunity kept this way. This cannot reduce the Taint points acquired below 1.
Finger of Jade
A finger of jade absorbs 10 points of Taint that its bearer would otherwise acquire. It will only absorb half (rounded down) of the Shadowlands Taint points if they were acquired willfully, such as through the use of Maho.
Tea of Jade Petals
If tea of jade petals is consumed, a player suppresses the effects of one Shadowlands Taint disadvantage for 24 hours. If tea of jade petals is used in a Tea Ceremony, add the following effect and new opportunity:
Effect: Each target suppresses one Shadowlands Taint disadvantage of their choice, plus an additional Shadowlands Taint disadvantage for each bonus success.
[2 opportunity]: Each target adds one kept [success] die to the next roll they make to resist acquiring Shadowlands Taint made within the next 24 hours.

FF - Please make Hi-Res files of Francesca Baerald's beautiful maps available for purchase/download! Those of us who use Roll20 and similar services would love to be able to use such highly detailed and frankly gorgeous maps to use when we play! Thanks in advance!  

Or accept that Rokugan isn't a capitalistic economical system.  It is a feudal agrarian barter economy.
Unlike the money as we know and use today, a koku doesn't have any intrinsic value on its own.  Instead it is a symbol (technically, an IOU but we'll get back to that.) for something that has value in Rokugan. Rice! That means you can't earn koku, you can only grow it.
(This is incidental the reason why money and commerce is seen as something dirty and unbecoming for a samurai. Rice is produced, grown, through manual labour and a honourable samurai should stand above manual labour. As a koku is a symbol for rice, it by association is also symbol for manual labour. So just as an honourable samurai should stand above manual labour he/she must also stand above money and commerce.)
So how does it affect the economy in Rokugan. In other words, how does it all work.
To start with no rice, no koku. This is a literal truth. Each koku represent the amount of rice it takes to feed a peasant with rice for one whole year. (In the real world in edo period Japan that was about 5 bushels. Don't ask me how much that is.)  Each great clan mint their own coinage each year based on their harvest. Minus what they owe in taxes to the emperor. Why minus what they owe in taxes? Because the tax to the emperor is literally paid in rice. So each clan have to lug thousands sacks of rice to the emperor to pay their taxes. (And I assume that based on the rice he receive the emperor in turn mint his own koku.)
So let say, the great and awesome Pokemon clan grows a 1000 bushels of rice a good year. Now the emperor will want his share which will most likely be a lions share, let's for the sake of convenience say half but it would probably be more. This leaves the Pokemon clan with 500 bushels of rice to mint koku from. Except they need to eat some of the rice to survive so in the end they only have 200 bushels left. 200/5 = 40. So in the end the Pokemon clan is the not so rich owners of 40 koku to trade with.
Unfortunately, next year there is a drought and the Pokemon clan only managed to grown 800 bushels of rice. Oy vey.   Of course the emperor still require his cut of half their harvest leaving them with only 400 bushels and they still need to eat. Can't let the peasants starve to death as they are needed to grow the next year's harvest. No peasants, no harvest and the clan is bankrupt.  So the bad year the Pokemon clan is only able to mint 20 koku. The bad harvest literally cut the clans fortune in half.
Of course, not all clans is as lucky as the Pokemon clan by being able to grow their own rice. The Dragon clan's lands are located in the mountains of Great Wall of the North, which isn't exactly good rice growing country. Yet the tax to the emperor still have to be paid in rice. Luckily, the dragon clan have rich mines. So they instead of grow rice, they mine iron and then goes to their good friends the Lion clan who has fertile rice growing lands and says; "Hey buddies, you want to go to war and need swords for that.  You grow more rice than you need on your lands but you can't grow swords. Luckily, I have all the ore for swords you need and I will give the ore for all the rice you can spare."  And so the two clans barter ore for rice so that the Lion can go to war with new swords and the dragon can pay their taxes.
And most commerce and trade in Rokugan has that character. A straight up barter of goods. From the peasant trading a chicken for a new knife to a great clan trading a valuable commodity for another, with rice being the most valuable.
The need for koku is rare and is generally only used when a person or clan doesn't have a commodity the other part wants.
Let's say the proud Lion doesn't want new swords as everyone knows that the old swords the ancestors used is so much better so they don't want to trade with the Dragon clan for ore. Luckily, the Phoenix clan wants the Dragon's ore for bells in their temples and shrines. Now the Phoenix clan can grow their own rice but only enough for their own needs, in other words enough to pay their taxes. However, as fate would have it the Phoenix clan just traded a bunch of wood to the Crane clan to be made into three-ply toilet paper as the Crane clan is far too sensitive to use mere two-ply paper. But as mentioned the Phoenix clan grows all the rice it needs so the Crane clan gave them a large pile of koku instead of rice.
Now, the Phoenix clan can't give the Dragon the rice it needs but it can give the Dragon clan the koku it got from the Crane. So  they trade ore for koku.
Of course, the Dragon still needs rice so it has to go to the Crane clan and say; "look I got a pile of your koku. I want the rice this represent." And the Crane clan has no other choice but to hand it over or admit that they are cheats and frauds and that their coin doesn't have any value. So naturally, the Crane take back their koku and happily give the Dragon rice instead.
Which shows how koku is nothing more than a symbol for rice and  how it's value stems from it being a substitute, an IOU, for a fixed amount of rice.  Unlike a gold coin in DnD  whose value comes from the amount a gold it contain or a dollar whose value comes from what certain economical institutions agree on what it value is. 
Which in turn is a segue to commerce in Rokugan. A clan needs more than just rice to function. It needs steel for tools, weapons and armour. Jade and other precious stones for protection and jewellery. Wood for construction and paper. And so on.  Most of which they need to turn to another clan to get or rather trade. Most of the time it will probably be a straight up trade or barter.  Other times koku is substituted as payment. But the purpose of every trade, every deal is to provide for the needs of the clan.
Unlike, in a capitalistic society like our own, the goal of commerce in Rokugan isn't to make a profit but to ensure that the clan has everything it needs to function. Once it that is accomplish there is little need for any further trade. The reason the Crane clan is one of the most powerful clans in Rokugan (at least before recent events in the lore) is because it is largely self-sustaining while producing a large surplus in rice. Instead, of lining their coffers by selling the surplus for a profit as we would expect in our society, they give the surplus away as gifts to less fortunate clans in return for future favours in court. Essentially the Crane pay the other clans' taxes to get their support in the emperors court. 
The focus of commerce on providing for the clan's needs instead of profit is the reason there are no real merchant guilds or independent merchants in Rokugan.  At least not above the level of shop owners or itinerant peddlers. If you trade in bulk you most certainly does it in the service of a clan.  Of course, since money equal labour which a honourable samurai should be above, the clans need Bonge middlemen to act as merchants though under the strict guidance of a Samurai patron.  But even they should take care not to do it for a profit.
Naturally, every one wants to make a good deal and it's only human to want something extra for your trouble (especially as a bonge merchant) but to be in it to make as huge profit as possible is more than frowned on. For a Samurai it can even be against Bushido. It is the reason way materialism is something negative for a character. For the same reason a very dutiful and honourable samurai patron might not take or receive anything extra from the commerce he/she controls, being perfectly happy with what his/her lord provides. 
Now why might that be. It brings us to the feudal part of Rokugan economy and player characters personally economy.  The most valuable commodity is as we have establish rice. The reason for this is because rice comes from the land and all land in Rokugan belongs to the emperor making it sacred. Thus all rice in Rokugan belong to the emperor and everyone else, from the lowest hinnin to the loftiest Clan Champion, is there to serve the emperor by taking care of the land. In return the emperor graciously grant every person in Rokugan a suitable stipend for their station in return for their service to him and the land.
A peasant grows the emperor's rice and in return is allowed to keep enough food for his family to live on until the next harvest. A local lord collects the rice and administer the villages under is charge and in return is allowed to live in large house with servants to care for his needs and ji-samurai to help him protect the land. The local lord gives the rice to a provincial daimyon, who in turn maintain the province infrastructure and keeps an army for its defence. For this the Daimyon receives a castle with hundreds of servants and samurai to assist him in his duties. The daimyon gives the rice to the clan champion who gets a even bigger castle and in return gives the rice to the emperor. Who, assumedly, spends most of his time eating a **** load of rice.
Now practically this stipend comes from your clan and is granted by the guy above you in the hierarchy but technically it comes from the emperor. 
Which brings us back to the problem with making a profit.  By making a profit you are taking more than your share of rice and the guy you're taking it from is none other the the sacred Emperor himself.  Making a profit in Rokugan is literally stealing from god.
Which finally brings us to the OP's question "How do you Koku?".
The short answer is: You don't. You just don't steal from god.
The longer answer is: You don't because it is assumed that your lord has provided you with everything you need to perform your duties according to your station. This includes full room and board, medical services, clothing and any other accoutrements you might need.   If something breaks, you go to your lord for him to replace it or pay for its repairs. If you duties change so you need new equipment you go to your lord for him to grant it. If you lack something you need to perform your duties, you go to your lord for him to provide it. And if he doesn't you can protest to your lord, hoping he will change his mind. If he doesn't you can either accept it and make do, keep protesting by either leaving his service by joining the Brotherhood or committing seppuku. Unless, you think his refusal is gross negligence in which case you can go to your lord's lord and complain. In which case there are really only two outcomes. Either your lord's lord agrees with you by making your lord commit seppuku for his negligence with you doing the same next to him for ratting out your boss. Or he disagrees with you  and you still have to kill yourself for telling on your boss.
Of course, the stipend often include coin in the form of a few koku. Someone mention treating the starting koku as an allowance.  I'd say that is spot on.  Normally I'd say that represented the amount of a yearly allowance because that was basically what it was. But because of the actually prices in the rulebook if I ran a game I'd probably treat them as a monthly allowance. (1 bu for a bottle of sake is the real world equivalent of a 1000 dollar bottle of champagne).
(Don't forget that the 4-5 koku you get is really a crap load of money. 1 koku represent the amount a peasant need to live on for a year. It is a year's wage for a peasant so as a samurai that coin is equivalent of a 6 figure salary in the real world.)
Now you're not supposed to use the money to buy equipment or stuff you need for yourself. That would be insulting to your lord. Basically, stating for anyone to see that he is unable to care for his subject and claiming he is unable to perform his duty.
So what do you use the koku for if not for stuff for yourself. Mostly, you use it for gifts and entertainment. Gift giving is important so most of the stuff you buy should be for others including your lord. Of course, going to a tea house or the theatre isn't free but everyone even samurai needs to relax and enjoy themselves at times. (And bullying innkeepers to get free drinks usually only works once or twice.)
The koku is also there so you can support yourself when your lord can't do it directly. For example when you travel through another clan's lands. Your lord has no power to provide for you there but through the allowance he can still do so indirectly thus fulfilling his obligation to you as his lord.
From a gaming perspective, forget about players earning gold DnD style, forget about them going shopping for gear.  Just give them when you think they need and if they want anything else make them make their case in front of their lord and decide if it is good enough for him to relent, through dice rolls or roleplay  is up to you. And if they want something they shouldn't have just deny them.
They want a rope for a mission, just make them go to the castles store room and take one.
They're going to war, have their lord give the armour they need, and once the war is over have the lord take it back.
The courtier wants a cool katan like the one the bushi have. Tell him to forget it. It's not part of his duty and should never be.
And only make them pay cash for something when they are in a situation where their lord can't  or shouldn't do it for them.
 

To be honest, I agree. I would generally avoid a random encounter - that's not to say I wouldn't put in a "one episode" or "two episode" sub-plot; especially if it gave a specific character a chance to show off a comparatively obscure skill (depending on the setting, stuff like aesthetics or survival, for example), but I've never been a fan of "Suddenly, Orcs! Kill them because they have fangs and level-appropriate quantities of gold pieces!".
Even if the PCs get set on by random thugs in a sleazy town, the gang or at least their boss is likely to show up again later on in this or a subsequent adventure.

I don't get it. hard to understand, but doesn't it make the duelist with more composure simply able to destroy the other one all the time?

I think the design process should start with a clear goal.

Here is your goal:

The goal of this ruleset is manifold. First, I want Iaijutsu duels to stand out within the game. [it already does, but ok] 
 
In prior editions such duels were conducted as their own mini-game, which achieved this objective. [they still are their own mini-game]

Second, I want such duels to be quick. [indeed they can be slow]

Thirdly, I don’t want an Iaijutsu techniques to be mandatory (so characters can just use water stance). [Iaijutsu techniques are not mandatory at all for duels, you can always use water stance]

Finally, I want the rules to have the potential to be deadly. In prior editions, it was possible to die in a single stroke during an Iaijutsu duel. [a finishing blow is extremely deadly already]


SO, basically, your rules are way too complicated for the simple goal that you want to achieve: make duels quicker.

You need to be more precise about your intentions, and nail the issue on the head in one single moment. Probably that your issues with Dueling in the system are not as wide as you think. Reducing the lenght of the duels wouldn't require that much changes.

I have noticed modern RPGs rarely make the Important Experienced Super NPCs anything super stat-wise, so it does not surprise me that Toshimoko would be a push-over as written.
However, I would also assume the venerable Kakita sensei has at least Martial 5, since the Core Book has separate sidebar discussing that Rank 5 at skill is not the final pinnacle of achievement in it. One more Skill Die is unlikely to completely change the encounter, but it would be more fitting for the character.

"Yes."

One would need some sort of local authority for it, but since ronin often lack higher protection even a yoriki could cause problems to them. If a ronin is attacking people or stealing stuff on Clan lands, there is no reason for the Clan to treat them as anything else than invader, even if they are alone.
Then again, Clan samurai will need a reason to attack ronin, at least plausible invented one.

Now receiving whispers on the winds that some people already have their copies - would like confirmation if anybody here has their copy. The reported schools:
Bayushi Deathdealer
Daidoji Spymaster
Doji Bureaucrat
Ikoma Shadow
Mercenary Ninja
Shiba Artist
Shika Matchmaker
Shika Speardancer
Togashi Chronicler
Yasuki Yojimbo
Reported titles:
Castellan 
Covert Agent 
Dreaded Enforcer 
Esteemed Negotiator 
Kenshinzen 
Kyuden Asako Shieldbearer 
Master Artisan 
Winter Court Champion 
Seven Fold Palace Acolyte

My general understanding is that in general a decent chunk of what Courtiers do is to find casus belli (or work later to refute it). The land may be owned by the Emperor, but it is leased to the clans. Some of these areas have been leased to clans for a very long time. And how these leases are determined involves imperial maps - which as we know are not always true-to-life accurate. 
Some will engage in realpolitik. You are Dragon, experiencing a famine. Lion have a lot of wheat fields, and you can't wait for them to be nice about it - you'll occupy the field with some Mirumoto and pay them back later, and if soldiers show up, you'll bonk them on the head and run back to your mountains. Peasants have founded a new village along the border tapping a natural resource - such as a new logging town, a river port or fishery, an iron mine. The maps don't technically have this on them yet, so you want to occupy it with some bushi, declare it's your territory and then schmooze the Miya to have them draw it on your side of the border next census. If your neighboring clan thinks of the same thing, you might have a skirmish. 
But, Honor can also enter into it a lot. 400 years ago, some Miya or Ikoma or whoever drew a line across this valley saying Scorpion on one side, Crane on the other, and there's no natural border inside the valley itself. So in this box valley there is a Scorpion (Red) Castle, and a the other a Crane (Blue) Castle. The two houses of these castles have been arguing for hundreds of years about who owns what in the valley - occasionally they come to blows. The territory itself doesn't matter - unless you draw a new map the valley is split, but those darn dirty Reds and/or Blues keep mocking you and trying to edge you out of your territory. Maybe you're a Lion lord, and your cutest most precious younger sister has fallen in love with the suave, cool, perfect Kakita lordling across the border, and they've eloped - his Lord allows this because it gives him an in on her inheritance. But more importantly she's bound by honor to marry somebody else and also, dude, it's your sister. So you'll marshal the banners and march across the border and if they don't give her back you'll knock over their castle. And once you get a bad blood going, Samurai don't need any pragmatic reason to get into an argument with those guys across the street, because a few generations ago they insulted your great-great-great-grandmother or accidentally killed an ancestor in a duel. Institutional memory is long, and understanding and worship of ancestors empowers it. And probably remembers the other guys as less honorable than your guys. Except maybe if you're Scorpion. 

From Core Book pages 22-24, the sequence of check is declare intention, determine details (Skill, Approach, TN etc.), Roll, modify Rolled Dice (Advantages and Disadvantages etc.), choose Kept Dice, resolve Kept Dice.
I would rule Mirumoto school ability is chosen before the roll, since the ability is triggered by character being targeted. Being targeted is part of attacker declaring their intention to hit the character.

It seems to me that there is a tru here to stop the "monopoly" on certain category of concepts. The Wasp were the only archery specialist, now you have the Kaito to. The Scorpion had the only Shinobi, now the Cat is here. The Crane were the matchmaker, now you have the deer... I think it's a good idea to let a little more option to a player who want to play with a concept but not be limited to only 1 Clan because "there are the only ****** of Rokugan"

I also would assume some sort of illusion of neutrality, especially if the Deer is brokering a match between clans. Or they avoid the truly big matches, so Great Clans can fight and plot over those and nobody is bothered by the Deer clan.
There are plenty of minor clans lacking nakodo, ronin and less important Great Clan samurai who are beneath notice of their own clan's nakodo.

I also would assume some sort of illusion of neutrality, especially if the Deer is brokering a match between clans. Or they avoid the truly big matches, so Great Clans can fight and plot over those and nobody is bothered by the Deer clan.
There are plenty of minor clans lacking nakodo, ronin and less important Great Clan samurai who are beneath notice of their own clan's nakodo.

Hello there
I made myself a cheat sheet to ease the use of honor gain/loss during play.

I share, feel free to comment 😃
https://www.dropbox.com/s/6wlfypi1b06tiub/the_tenets_of_bushido.pdf

There are a few different forms of duel in Core Book. In legal iaijutsu duel with official challenges and permissions from higher lords only weapons allowed are katana and wakizashi, so calling kami to help would be against regulations. The book also makes point about shugenja being rare and valuable, thus their lord is likely to forbid them from fighting in sword duels and may give them a yojimbo for this.
As others have pointed out, there is also more informal form of dueling called Warrior's Duel in the book, which has far fever regulations and basically just boils down to shouting a challenge and charging with whatever weapons you have. Calling kami for help in those could be perfectly allowed, if one sees them as extensions of shugenja's skill and will.

Let It Ride (rule taken word for word in Burning Wheel RPG)
One of the most important aspects of ability tests in game play in Burning Wheel is the Let It Ride rule: A player shall test once against an obstacle and shall not roll again until conditions legitimately and drastically change. Neither GM nor player can call for a retest unless those conditions change. Successes from the initial roll count for all applicable situations in play.
A GM cannot call for multiple rolls of the same ability to accomplish a player’s stated intent. Nor can a player retest a failed roll simply because he failed. Tests must be distilled down to as few rolls as possible. The successes of those rolls ride across the entire situation, scene or session. If a player failed a test or generated no successes, the result stands. If he was hot and got seven successes, those stand for the duration.
 
 
Sweet and simple! the GOLD line in there is: "Tests must be distilled down to as few rolls as possible" 
Gosh I derailed that thread....
Anyway, I invite you to try that in your L5R games for any scenes outside skirmish/intrigues (which are basically "action sequences" in which you can try to bash a door twice because there is a sense of danger/time etc being a conflict scene).

That's basically it. The Merchant themselves has next to no legal rights and hence anything you do to them isn't  a problem. Inconveniencing their lord, by taking large chunks of money and/or bodily extremities from the merchants who keep the economy of their town running is the sort of thing that even a "I don't muddy my hands with trade" lord is going to be aware is a bad thing to allow to happen, and may object.
 
To me, it's the same logic as paying for a room in an inn whilst travelling. Yes, you can just demand the room.
But it's going to inconvenience a lot of people and some of that inconvenience might ultimately splash on someone higher up the social scale than you - the innkeeper's lord, their lord, the next (invited) guest who should have been in that room, whatever. A totally-not-a-commercial-payment "gift" in thanks for the innkeeper's family and the town magistrate's troubles in accomodating you at short notice sooths ruffled feathers and prevents that ever being an issue, since the inn can afford to replace the food and sake you consume, a merchant guest can be offered a bit of consideration to give up their room in favour of a hayloft or something to create a spare room, and no-one is significantly put out. 
 
The same is true with loans. Yes, you can walk into a prosperous merchant's house in your lord's town and say "I'm taking all your money", and they have no legal answer other than "yes, sir, no, sir, three bags full, sir."
But when tax day rolls around and the town magistrate says "where is your money?" They can answer honestly "My lord's samurai took it" which if this is a regular thing, results in tax revenues gettng messed up and the people running the province being noticably more short of money than they should be. Inconveniencing a merchant isn't a crime. Noticably inconveniencing your lord is. 
Hence, a different approach is to take the money on a temporary basis, on the understanding that you will return it and not defraud your lord of their due tax revenues. 
The problem comes with how much you actually take and how much you owe when you come to pay it back. After all, the value of a Koku varies between clan territories and on a yearly basis, and on a far more dramatic basis than currency variations in modern economics. Since - as noted in the original post - an organised cartel of local merchants basically controls the price of rice, and a Koku is nominally "the value of a defined chunk of rice", they can basically devalue or inflate the currency between the time you borrow the money and the time you pay it back (depending on whether the loan is recorded as an amount of coinage or an amount of rice). 
 
 
Accepting interest payments is the one rogue bit here - whilst a merchant can make a pretty defensible argument for handing money over as a loan (unless you've got or get approval to take the money from your lord), charging interest on it is a different thing. That, by comparison, is only possible if the merchant thinks the lord and magistrate will back them because that is the classic "I'm charging money for nothing" which throughout history (occidental as well as oriental) has made moneylenders a socially and religiously villified profession.