I like the idea Bruce.
I think the Phoenix is a really good way to go in your tale. It keeps the two sides separate as they evolve too which is a nice imagary. I think it works on a number of different levels.
As for there being one Phoenix - in our mythology maybe - but this is your world so go for your life.
You're already covering the giant lizard/dragon angle with the bad guy and your theory regarding evolution is sound so why not a giant bird?
Good luck