I would not enlarge the time scale too much. At the 10 000 years of pace, farmers could move hubwards every few generation, but farmhouses, even proper log ones, deteriorate anyway. Cities do have some problems in that geography, at least in coastal areas, is presumably changing swiftly enough that a century would alter the coastline completely, but that ought not be a setting-breaking problem, merely a challenge. Why not let the long-lived folk be more nomadic in mindset? Dragons might migrate with their hoards, making themselves large obvious targets to adventurers and rival dragons alike.
Do you intend to have nine primordials, as you have now, or eight, as seemed your original statement and as is still written? Why include alignment nonsense at all if the greater deities are beyond that?
I strongly advise a small selection of gods to having all gods from any book, ever. That would lead to a mess - cities would have temple districts that stretch on seemingly forever even if the gods, instead of having individual temples have small shrines and chapels within a greater unified complex instead. Too few options is constraining, yes. Too many, however, dilutes the whole setting. The same goes for creatures - there are so many various monsters in D&D that including a moon solely to have lycanthropes, unless lycanthrophy is a major theme, is needless. You do not need to make a 'main' campaign setting like Forgotten Realms where anything goes, or do you believe otherwise?
It would further be interesting if the simple gods' similarities to the primordials, not any arbitrary divine ranks, determine how mighty they are - Kokopelli would clearly remain a greater god, a more 'complete' fragment of primordial chaos than most others.
As for Asteleben, while I like the idea, how likely is it that a pre-renaissance civilisation would even have a concept for evolution, let alone on a world where any absurd crossbreed is possible?
Before focusing on a sun-god and moon-goddess, I advise considering how the damn sun and moon(s) even work on such a world. Does the sun rise and set, effectively making this world an oddly-shaped planet? Is it a glowing magical orb somewhere out there which periodically lights up and dims to the point of complete darkness? You seem to be mixing nice and interesting ideas with old and rather stale ones.
Violence, if kept with CE ought to see madness, paranoia, hate and cruelty encompassed within it.