I am probably missing something obvious, but it sounds like a combination of your two origional ideas would work. Specifically...
Cut the appropriate amount down on the walls and remove the roof/unwanted wall pieces all as one piece.
Remove all the rivets holding the side walls to the origional roof, and peel the top portion of the side wall off the roof. I am assuming that it is caulked and will otherwise be difficult to remove, but you can peel it back in sections, you don't have to remove it all around in one shot as per your origional proposal #1.
Now with the top side walls removed, and the caulking residue peeled away from the origional roof, you can lower it back down on your lower side walls and attach it, per the 2nd part of your proposal #1.
The problems I see are:
1. I have no idea how the underlying side wall structure integrates with the roof structure. Dropping the roof onto existing walls means everything has to be perfectly cut and trimmed and ready to join. There also has to be a way to tie the structures together. I am assuming that this involves more than just riveting the outer skin to the roof. The inner structure must attach as well.
2. Getting the roof to slip down and inside the side walls might be frustrating. I can imagine that the side walls will bow and wiggle and keep getting under the roof rather than slipping around to the outside all the way around. You might need 10 good friends to help massage the side walls outward as you lower the roof down. Sometimes putting together things piece by piece is easier than trying to get really big heavy pieces to fit just right, especially if you are working all by yourself. There is also the issue of how you get a really watertight seal between the new lower wall and the roof. You would have to caulk the two surfaces and push them past one another which would probably mostly push the caulk out of where you want it.
I am assuming way too much here, sight unseen.
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