Regarding Epic Bonus: You add it once, to the ability modifier. I realize now that I probably didn't word the well in the OP.
However, after I finish these drafts I am going to revamp the system a bit and the epic bonus is probably going away to be replaced with epic/divine ranks. The epic bonus was a method to separate epic monsters from regular monsters & PCs, but it is not very 5e and bounded accuracy. So I think I can solve both problems with divine ranks.
That sounds like a really good idea. Divine Ranks do feel like something that's missing. I'd recommend checking out the old Deities and Demigods book from 3.5
How did you decide on HP for the deities? It seems to mostly be their HD + 9 x their HD number and then + their constitution modifier x constitution score?