Fantastic, I've been waiting for this!
A suggestion for religion and civics if you are going to be including non-humans (please do!): add two more; Alien and Anti-Imperial. These would, obviously, only be available to non-humans. I base this on the Tau, Eldar, Necron, Orks (I don't think they're Chaos at least?) and Tyranids, because none of them are Chaos, but they are all either not Imperial and seek to live their own lives free of the Emperor (represented by Alien religion/civic) or they are fiercely against the Imperials and wage unrelenting war against them (represented by Anti-Imperial).
I'm not sure what to include for the effects of these... but I think a good start would be that Alien makes +1
and Anti-Imperial makes +2
for all Imperial Civs. Also, I think that Alien should be able to convert back to Imperial, because they haven't really declared themselves full enemies of the Emperor yet, but Anti-Imperial should lock out Imperial. It shouldn't lock out Alien, however once they've gone to Anti-Imperial they can never return to Imperial, even if they do convert back to Alien. I don't know if this would be possible, but I think it would make the game a lot more exciting and true to the WH40K universe.
Also, in relation to Chaos, I think it should be possible to convert to it from Alien or Anti-Imperial as well, but once you convert to Chaos you can never go back to a non-Chaos religion. Chaos Undivided I think should be unavailable unless you have converted to Chaos first (but it would be possible to convert back to normal Chaos).
That's just my take on the situation anyway! I'm certainly not trying to dictate how you make your mod, but I hope you might take into consideration my suggestions! Thanks!