Hi there and welcome,
I have a rather different view. It is your game and you can do what you want to but I have some serious doubts about your proposed setup.
Straight off the bat, I foresee problems with skills. Only War is focused on (squad) combat while Dark Heresy is focused on investigations. If you start your players are guardsman, they will lack the necessary social and investigative skills later on, much akin to having an entire cell consist of Dark Heresy guardsmen. If they can only swing a hammer, every investigation is going to seem like a nail which means your adventures will become rather repetitive. Then there is the fact of your proposed origin; the inquisition already has its own human ‘army’; stormtroopers in addition to Grey Knights, Deathwatch and Sisters of Battle. What possible niche are your troops supposed to fill which isn't already covered? Besides, if you start your men out as elite soldiers what is left for them to strive for? Getting better loot is an important part of rpg-ing for many players.
Canon wise anything is possible. But it makes little sense as the inquisition already has droptroop commando’s, namely its own stormtroopers. There would be little reason to raise a new regiment to do the same. Any inquisitor can already requisition stormtroopers. And if he can't get those, he also won't be able to get a full regiment as higher commanders would check his credentials first before submitting. You could off course flesh out the stormtroopers and then have your players pick this as their regiment. But it seems to me as if you are trying to play a Dark Heresy game with Only war characters. This way, you are deliberately eliminating a lot of diversity. Dark Heresy offers a lot of background packages which can all be used to shape characters in unique packages with diverse skills.
Inquisitors use regular troops for main assaults (for example on a cultist stronghold). These troops can either be requisitioned for a specific mission (e.g. borrowed from the nearest Inquisition stronghold or from the closest PDF or IG force) or the Inquisitor could permanently attach a squad or platoon of troops to his retinue. A cell of acolytes however is an entirely different kettle of fish. Their task is to do the donkey work or solve minor problems, leaving their boss to focus on the big stuff. They don’t normally accompany their inquisitor but are sent out on their own. The fluff makes clear that inquisitors pick individual candidates who can act independently and get the job done and whom have caught his eye. In short, it is very unlikely that an inquisitor would pick an entire squad and make them acolytes. Far more likely that each individual comes from a particular regiment and did something to catch the attention of the inquisitor. If you really want them all to be guardsmen from 1 particular regiment, you could have them perform some suicidal, heroic act which kills off most of the squad (such as fighting and banishing a deamon or a major heretic). The survivors might be picked up by an inquisitor…In any case, having squaddies would make everything more complicated. Get rid of them and allow the players extra skills or talents to compensate. I don’t want to belabour the point but I really don’t think your basic campaign idea of elite guardsmen using valkyries and jump packs (e.g. elite assault force) can work as an acolyte cell.
The salary scheme in DH is seriously broken IMO. Either give your players an equal flat fee paid by their inquisitor for all work expenses and living costs or provide them with basic equipment (gun, ammo, necessary equipment) and an expense account and include what they reasonably would need for a particular mission. If they abuse the expense account, slap them down hard. Smart players soon learn to ‘acquire’ stuff on their own, petition their inquisitor after a successful mission or simply go without.
The simplest answer is the DH Creatures Anathema. Each product line has its own monster manual which is specifically aimed at its own power level. You can adjust things yourself and sometimes the background is useful but the easiest solution is to pick the monster manual belonging to the product line itself. This one will also give examples of typical opponents for an cell of acolytes. Together with the DH corebook you are pretty much set and its easy to make your own opponents.
Rogue Trader has the jump pack listed while Citadel of skulls has stats for the valkyrie talon. There's a post about this on the forum. You might also consider searching online for the Apocryphy Vehicles.
I see what you are saying, but this is the kind of right in line with what I want to achieve with the campaign. You will have a set of characters that have trained and studied their entire life with the thought that their existence will be fighting the wars of the god emperor, the imperium and mankind only to find out that they will be asked to do those things in a way they were not prepared to do.
My idea, essitially is that they will do something particularly important or distinguish themselves in some way during a mission, which will basically be a short "prologue" adventure. This will catch the eye of the inquistor who deployed them, and the player squad will find that they have been appropriated by said inquisitor exactly as you describe. The squad will be the inquisitors personal asset that he uses to accomplish things that require less than subtle methods. Maybe the squad will be asked to assault the headquarters of an underhive crime boss--for reasons unclear to the characters--because the inquisitor wants a prisoner freed, the crime lord captured, or some data recovered. Perhaps there will be a mission where the inquisitor wants a certain quarded shippment of weapons or drugs captured, or maybe the inquisitor needs some protection for a high ranking agent that is going to negotiate with a warlord on a feral world.
Basically, in the first act of the campaign, I will be running it more or less as an actual game of Only War as I understand it, as I see no clear distinction between the kind of missions and themes that are present in the Only War book itself, other than, of course, the role which characters are playing. In other words, the first act will be an Only War campaign except instead of being a squad in an IG regimate at war, they will be acting at the behest of, and on the whims of, an inquisitor.
Act two is where you think the problem might be, but I think this might work. So you have this squad of "elite" IG droptroops working for an inquisitor--incidentally they will be "elite" only in the sense that they will think of themselves this way--who as time goes on has certain things happen to them. For one (I can't be specific because I haven't got that far) in the course of just "doing their job" they will learn hear, see, and learn things. They will also gain the "trust" of their patron and become relied on more and more to do things that are both out of their comfort zone and beyond the scope of their training.
This I think will be great RP wise as a number of questions can be raised and addressed. For example… how do the characters react to their growning understanding of reality? Does their devotion to the Imperium, "Duty," their inqusitor or themselves waiver? How do they go about seeking the training, knowledge and resources when they are asked to do things more in line with Dark Heresy investigations? Seeking out training, access to knowledge, tools, and building contacts is I think a nearly endless source of story hooks and adventure ideas.
I'm also thinking that, by in large, that they will be asked to do things that cause them to spend long amounts of time away from the regiment itself, so they won't be able tor rely on their logistics skills, or typical chains of command for gear. Often they will be given the freedom to assertain threats, then deal with them in ways that seem appropriate. This might mean months half a sector away from their "base" of operations, so they will have to be resourceful as far as getting the "tools" they need for the job once they figure out what that "job" is.
Does this seem to make sense and do you think it is workable?
For your first numbered point, I actually think this works great in my favor. I say this because the imperium and the inquisition is huge, right? So it might make sense that new regiments for the inquisition will periodically need to be raised. I mean, the way the book sort of makes it out, regiments that are depleted are replaced rather than reinforced, and even if that's not the case, as new conflicts emerge and new space is uncovered the imperium is always in need of new IG regiments. Why wouldn't the same be true for the inquisition?
Second point: I see what you're saying completely. Basically, as I said above, this is precisely the storyarc I want to work. Inquisitor permanently appropriates player squad and uses them for things that require a heavy hand. Eventually as time progresses, circumstance and performance change the way the inquisitor "sees" and uses the squad until the players are on unfamiliar ground.
Third point: This is what I think as well. My question I guess is--since I have not really played or GMed any of these games yet--what do you think is fair as far as monthly salary goes? I guess maybe I'll just figure out what the median base income is in the DH books and go with that. The expense acounts are a bigger problem, as I'm really I worried about giving them too much money, and thus making things too easy, or too little money and making them too hard. What do you think would be in the realm of fair?
Thanks for the other info. I was able to track down the homebrew Valkyrie stats on the forum post you mentioned. That was very helpful.