Wow. It's funny to see all the stuff you came up with AFTER I took Neruz's advice and went on a Lexicanum trawl.
I still need to look at the history for most of the races, but, man, is the Imperium screwed. Also, everything is the Eldar's, and the Necrontyr's, fault.
The Necrontyr's petty war with the Old Ones was what created the first bad warp things.
And the Eldar were so bad they tore the universe a new a-hole, which also had the effect of creating a new God of Chaos.
Da EMPRAH was immortal, and supposedly born from the combined souls of all the shamans (who were trying to avoid being eaten by warp-things when they tried to reincarnate). The Golden Throne was originally a teleporter-thing to traverse the webway, and yes, it does have irreparable faults. Should the WH40K plot ever advance, the Emperor will die, and mankind will soon fall to Chaos, tearing the universe apart AGAIN, and birthing a fifth (sixth?) Chaos God. Of course, he apparently had children during his 10,000 year or so lifetime, who are also immortal, and one nefarious dude plans on sacrificing them to the Emperor to try and revive him. All fun stuff.
Now to have a look-see at how the other races are shafted...
This is why I love WH40K!