I'll share the process I used:
Since I suspected that much of my rot was due to old cracked door and window seals, I started by replacing all of those (and rebuilding my "stack" windows). Next, I removed my entire interior, including all skins and insulation, lifted the shell, and pulled the frame out from underneath. Spent the next few weeks welding, repairing, scraping, and painting the frame. Pressure washed the interior of the shell trying to get rid of all the mouse funk. Prepared (ie, painted with poly on both sides and the edges) my new wood floor, installed it on the frame, and plopped the shell back on.
It was at this point I started my shell work. This included replacing the rear center panel, one of the front lower corner segments, rebuilding both of the front "wing" windows, removing the original air conditioner, putting a massive patch over all the rivet holes, and installing new AC. I also removed and patched the TV antenna hole, removed and patched the stove vent (since it looked like a mauled mess the PO had fabricated), and finally, since it looked like there was evidence of leakage, I removed the two roof vents and reinstalled them with a healthy does of butyl tape and vulkem. I also removed and reinstalled the refrigerator roof vent, resealed the plumbing vent stacks, and reinstalled my main awning.
After all that construction work, I reinstalled all the clearance lights, badges, and trim, and sealed all the pop rivets from the inside. I was feeling pretty confident that all my leaks should be gone now, so hosed down the exterior and looked for leaks. Sure enough, I found some, so I gooped every interior shell seam and row of rivets. When I was finally confident that I had no leaks, I went on with reinsulating and began reconstructing my interior.
My best justification for doing the shell work after the shell was back on the frame was that I suspected things may shift or change shape, plus I also figured with my luck, I might do additional damage to the shell during removal or reinstallation, and it would be especially sucky to damage a segment that I had just replaced.
It is easy to get carried away. I have heard of folks removing and reinstalling every window frame, or replacing lines of rivets "because they don't look good enough." Well, it is easy to create leaks--every rivet you drill out, you run the risk of creating an oblong hole that the new rivet may not seal completely. So I limited my work to fixing the things that were leaking and didn't reinstall anything that was water tight.
Been beating on this project for almost three years now, and still have a lot of interior to rebuild.