Thanks for the encouragement! I have to admit, I'm fairly amateur at all this and it's hard to keep myself motivated from just scrapping it. But, it's one of the better ones I've seen when looking at photos of things other people have repaired, so if they can do it, I guess I can too. I think what gets to me is that I feel like I will never find "the end" of it and will have to keep taking it apart until nothings left!
I ended up doing like you and pulled more off the back aluminum paneling and compartment doors. Mine has two 2x2 boards that go the width of the camper just under the entry door and the compartments. It seems the rearmost of those two boards is the only one that's rotten because the forward one seems fine. However, I can't fully see it yet, so I'm just wishful thinking at this point.
So, I think what I need to do to move forward is as follows:
Build a platform to set the camper on so I can take the rear jacks off
Remove aluminum skin on the sides to access the rest of the wings
Remove aluminum skin on the rear to access the vertical 2x2s in the rear corners the jacks mount to
Remove the rearmost horizontal 2x2 and replace it
Splice in replacement sections for the vertical 2x2s in the corners (how the heck should I do this?)
Replace the miscellaneous pieces that are the framework for the storage compartments
Rebuild the wing sections
Rebuild the very bottom valance type thing that covers the grey water tank
Replace the plumbing that was cut/damaged during the disassembly
Reskin the exterior with new plywood
Finish caulking everything