I'm not sure what to tell you about the plywood. In my case the bathroom skylight leaked and I was able to reach the damaged plywood by pulling pieces out from the edge of the skylight cutout and sliding replacements in. It's only 1/8" thick so you might be OK by just letting it dry out.
I've spent a lot of time researching leaks and recommended repairs and have decided to go the Eternabond route for the roof caps, vents, etc. After removing all the excess, and different types of, caulking from my front end cap, I was pleasantly surprised to see that the caulking between the cap and roof was sound. I covered the joint with Eternabond, which hopefully will last the remaining lifetime of my 2002 rig. I also used Eternabond on my new skylight and new vent. Next in line are the roof edges and rear cap, to be followed by the balance of the roof penetrations.
Before you go wild with caulking, make sure you understand the proper way to do it. You might want to read my post "Caulking Rant" on IVR2: