Well, just to follow up, I decided I had futzed around with this part of the project long enough and went ahead and bucked in the rivets this weekend. In the sections where the holes weren't lining up, I started out just drilling though the existing hole in the skin, but soon found that I was ending up with an oblong hole in the channel (where new hole merged with original hole), which threatened to not hold the rivet properly (a cleco wouldn't stay in the hole), so I ended up drilling new holes in both the skin and channel to thoroughly avoid any of the existing holes.
Anyway, its all back together now, just need to do skin repair in the rear where the original rear end separation was happening, and the back panel skin was rotten. More opportunities to improve my bucking technique.
Also on the topic of the home made sheet metal brake discussed above, I too tried building one like this, but found that I got rather rounded corners (on my .032" belly pan material), which weren't to my liking. I eventually found that by clamping the sheet to the edge of my work bench, and then just hammering the "fold" with a large rubber mallet, I could get a better, sharper corner. I also recently purchased the 30" sheet metal brake that Harbor Freight offers, mostly because it was on sale for 33% off. Haven't tried it out yet.