To repair the top plate in the wall, you will more than likely have to either remove the interior paneling or siding in that location.
The rafters will be attached to the ceiling so a manner of eliminating that fastening will be necessary unless you can jack the ceiling into position and sister-repair the rafters from above.
I buy a fair amount of aluminum and my local distributor sells vinyl coated aluminum sheet in various dimensions. The vinyl coated sheet goods offer some cosmetic upgrade and are easy to paint.
Sealants: Stay away from anything containing silicone. Rather than an off-the-shelf roof patch material, I'd suggest you aim for a polymer or urethane sealant. Geocel sells a variety of sealants for mobile applications, all of which are polymer based.
Eternabond tape is a great sealer, i have it on every seam on my roof. When I was done applying the Eternabond, I sprayed two coats of acrylic roof paint over the entire roof. If you are going to be coating bright, unfinished aluminum, a primer has to be used. I recommend Sherwin-Williams Industrial DTM primer, it is listed for bare aluminum.
Your budget could even be high for this project. Good luck.