So how shot is my roof?

I wonder if there is a place like David's Permanent Coatings near the OP's place. Replacing the rubber roof will be expensive, but it might be cheaper to have it done at a place like rvroof.com which not just uses epoxy spray to replace the roof, but it also does away with the need to caulk around skylights and such. It won't be cheap, especially if you have skylights and such replaced (might as well, as they are not that expensive, and they will eventually crack in a few years), but it will keep the rig dry for a long time, barring tears/punctures by branches.

Disclaimer: I've not used these guys, but everyone whom I've encountered who has had their roof done by them has had very positive reviews.