It was very interesting reading through the whole post even if it took me more than a week to return to it and finish it. I know what you're talking about, I have made lots of settings myself, although I prefer leaving them quite open to change until the time comes to fill in any particular piece of knowledge. Which is more difficult than in your case, not so systematic and prone to contradictions adding up in time, of course. Just my lazy impro style, I guess.

The thing that troubles me with your setting in terms of realism is...those periods of hundreds of thousands of years seem too long if we try and compare them to our civilization. Statistically speaking. This is some huge geological scale and I would normally expect civilizations to rise and fall faster than that.

And so would some players, I believe. Players love questioning your logic, don't they ;)

Have fun!