Re: STID and the Eugenics Wars books
My memory is a bit sketchy (Greg - can you help out ?), but I don't think there is much of a problem - the major changes are post revival which can be seen as due to the new timeline. The 'magic blood' could just be something that we didn't know about in the original timeline, or something Bones did to it in STID.
I don't think there is any way to reconcile the new comics back story for Khan though.
Soon oh soon the light, Pass within and soothe this endless night, And wait here for you, Our reason to be here...