OkeeDokee!I don't have a compelling reason to remove it yet. Only the edges were rotten. Originally I was planning on covering the whole roof with a black plastic sheet but I started painting it and thought it looked pretty good. For waterproofing, I gave it a three coats of exterior house paint over the one coat of 1-2-3 primer. There are a few small cracks left -- I plan to fill with silicon caulk. It rained overnight I inspected it this morning...even without sealing all the cracks it was bone dry inside this morning.
Someone suggested a metal roof, and I may still do that later, but one of the goals of this initial coop is to spend as little $$ on it as possible. So far, I spent $50 on the treated 8x4 floor and ~$80 on paint, screws, bits. The hinges were a gift from Dad and all the other wood was leftovers from the previous owners.