I think that Slaanesh could fit pretty well as RB, tbh. You could flavor the Dark Eldar as WRB and the Eldar as UG, if you're okay with being cute about it. This would also help out your color balance as currently your only occupants of Green are the Tyrannids and the Orks. T'au could also fit anywhere into Bant, IMO, as Green is all about harmony and finding your place in the world.
But you clearly know a lot more about the lore than I do, so feel free to disregard this advice! If you want something more tangible, I'd say to just start designing cards and go from there. Do you have any specific mechanics you're looking to use, or anything you've come up with? Personally, I've always thought that Madness would be perfect for in the 40K expansion, but it's pretty far from your skeleton.
Finally, when in 40K lore are you basing this set? Pre-Horus Heresy, or "present day?" What's your upper limit for who will appear on cards--Primarchs? Gods? I think that finding a narrative structure for it will really help tie the room together, so to speak, much more than any color/type balancing will.
I'm really interested to see how this turns out! Good luck!
Great questions and thoughts!
My overall plan was to have Dark Eldar be Black/White/Red as you suggested. The Orzhov side being the more aritocrat type Dark Eldar and the Rakdos side covering the fact that the Dark Eldar are the "fastest" faction in the galaxy and strike unexpectedly, without warning, and with incredibly speed and aggressiveness. So it easily fits into both.
Meanwhile there will be Eldar that are both Blue and Green, per your suggestion. The Craftworld Eldar will be blue, and then there are Eldar known as Exodites who life ascetic lifestyles and will fit well with green.
Green is tough though. The Warhammer 40k universe is very dark, ugly, and not too concerned with the preservation of life. So fitting people into green is tough. Though in addition to the Orks, Tyranids, Exodite Eldar, I think I will also include some Imperial Guardsmen like the Catachan Jungle Fighters.
I don't have any mechanics yet that will be unique to this cube. I have thought about some but that make be easier to implement on a 2nd draft so to speak. I agree about madness and I am hoping to incorporate at least a Dimir madness theme. Possibly extending it to Red a little bit.
Your last question is a good one. It is one I have thought about and not 100% sure the answer. As far as time period, I think my first inclination would be to say it is "mostly" in the "present day" of warhammer 40k. Which is to say the "Era Indomitus" so basically at the same point as the lore currently is. The Horus Heresy would obviously be the coolest time period to feature but it becomes somewhat restrictive because the T'au, Necrons, and Tyranid were all not present and the forces of Chaos weren't that well developed at the point. I also don't think doing a fully 100% Era Indomitus would be ideal because there are some characters and stuff that I want to include from different points on the timeline. So I think it is going to be kind of fungible. For instance I already created a card to represent Sanguinis even though he is dead. But I will mostly be trying to to delve in the "past" too much.
As far as upper limit I am not sure. The power band within the 40k universe is so wide that I have to be careful. For instance, a Primarch, in theory, is so godlike and beyond even a basic human that it is tough to include them in the same set. Like a Primarch is in theory worth like 20 regular space marines, which themselves are superhuman. But of course I don't really HAVE to 100% operate within the 40k power band. I originally did not think I would include anyone of the Primarch level but as I mentioned I did end up creating a Sanguinis card so I think I may include several of the Primarchs but I am thinking that will probably be the upper end. I had to basically tone down how powerful Sanguinis would actually be. His current design is this:
Sanguinis, The Great Angel
3WW
Legendary Creature -- Superhuman Commander
4/4
Flying, Vigilance, Lifelink
When Sanguinis, the Great Angel enters the battlefield, put one +1/+1 counter on up to 3 other target creatures.
"He has the vision and strength to carry us to victory, and the wisdom to rule once victory is won."
-Warmaster Horus
Not really that creative or anything but was supposed to just be a card that is either "good stuff" or a control finisher but also fit in with the counters theme which is supposed to be anchored in white.