Alrighty, haven't written much concerning the campaign over the last month (damn slump! damn presentation!) I currently do feel like addressing your points, because they are quite valid.
First of all as some sort of disclaimer, I've only really been into 40k since... think it was 4th edition? So any fluff before that is... something. Oh, and then there's of course the malleability of the fluff, which is something we can agree on without any further discussions, no?
This starts with the account on the War in Heavens and the Swords of Vaul: The only thing I made of the various sources which seem to be... somewhat certain (correct me if I'm wrong) are that Vaul had to build 100 Swords for Khain, 99 of which were awesome Ghostblade-thingies of maximum power, while 1 was just a normal, mortal sword cause Vaul couldn't hit his deadline. Khaine went to war against some enemy, but due to this one inferior sword, his line crumbled, he lost the battle (or won it, he still survived) then proceeded to show Vaul his "Gratitude", who build the legendary sword Anaris and waited for Khain (or the other way round, he first got Khaine'd and then build the sword in order to exact revenge, seriously, Eldar-Fluff can be as hard as reading Kant at times). Then at some point comes the War in Heavens, blahblah, Eldar-Gods die except the Laughing God, Khain in some way and apparently Isha.
However, how I like to see the Eldar-Fluff, is mostly them being Legends. Legends and Stories of things in the far, far, faaaaar past, and I do believe most of those stories have been significantly altered, but still having a true core, telling about events which have transpired, but are now nothing but Legends. So what I did is create possible true events based on that Legend.
Oh, and that other thing also comes from my interpretation of Chaos
I like to think that Chaos is... less "Four Gods conspiring against humanity and all live" but rather a "primal force of the universe, not inherently evil but twisted by whatever due to whyever". The division into the four domains for example is something which really grinds my gears: Why aren't there more unaligned entities? There's just so much potential lost, in my opinion.
Returning to the weapon: Well, the Eye of Terror has been around since the fall of the Eldar... but the Array is around since the War in Heavens, which is... probably quite a bit longer, no? And, again, the EoT is more of a(n) (un)natural phenomenon then anything else in my eyes, with the Anaris-Array being an actual weapon. Trying to find a fitting analogy... ah, let's assume the EoT is a Typhoon, mostly staying in one place, over the sea, blocking a few important trade-routes but in general being more of a nuisance rather then a real threat. Now imagine another Typhoon which has some sort of control-center, which deliberately targets ships and is generally enough of a jerk to not only interrupt your trade-routes, but actually follow them and wreak havoc in you trade cities and... pretty much everywhere else.
TL/DR: Valid points, but not my interpretation of the Fluff, so nope, I'll continue to build my own Frankenfluff (I must say, I like that word )
Oh, and while I'm posting here, anyone got a nice idea of whether the aftermath of "Haarlock having retrieved the Radiant Prince from Malfi" would be better of as a survival-horror "Madness unleashed, street-apocalypse"-survival horror adventure or more of a "okay, let's see if someone knows something and how many honourable duels we have to win in order to meet that someone" intrigue adventure?