Interesting ideas there.
I look forward to seeing what you turn out.
In my story, I still had the Cylons created by (and subsequently wiping out) an alien race.
The war with the Cylons had been going on for about 100 yahren (rather than a thousand), Adama is an admiral, (Boomer and Starbuck are dudes again), and the Galactica is a brand new, state of the art warship, creating a new class (and sadly, she is the only ship of her class) of battlestar.
I've gone over the details many times in the past. You might be able to find some of them in past posts I've made.
(Or you might be able to find it in the fan fic section of this forum).