Great suggestions so far, thanks. Calamus, how did you "patch" your roof? Did you actually fix the water damaged wood under the rubber roof membrane or just patch over the rubber?
Scott, what an epic project that was! Obviously you've been deep into the structure, if I wanted to cut out maybe a 2'x2' section of roof and replace the wood under the rubber how would I go about that? Going in I'd have no idea where the underlying structure is, or any idea how to fasten in the wood patch. And it isn't something I'd want to figure out as I went either, I'd rather have a solid plan before I started cutting stuff.
No one has weighed in on which Eternabond product I should be using. It seems like WebSeal is the right stuff if I'm going to be coating over with something like Liquid Roof or the Dicor EPDM coating, is that correct?