So, this is what I did. My flashing trim piece was in two pieces, so I think that made it a little easier. After drilling out the rivets, which was easier than I thought it was going to be, except for the 3 or 4 that were in The middle above the storage box. Those took some time and some contortionist moves.
The main run is flat with an aluminum frame topped by plywood top and bottom. The rivets were in the metal frame piece. At either end, there was an angled plywood piece, about 1.5 inches thick. They riveted the seal and trim piece in to the plywood on the ends, which was not a good idea as it separate the laminated pieces of plywood and allowed water in. There was a little rot.
I filled the holes in the wood, then epoxied all the wood surfaces I could reach. I put an index mark above a few of the holes on the flat part. Stretched the rubber piece down the whole length. I then was able to hold the rubber piece on the trim piece(there is a 1/4 inch lip on the under side of the trim piece) hold it up, and indexed the hole in the trim to my index mark, then used a self drilling screw with a rubber washer in to the existing frame hole. The beauty was that the self drilling screw went right through the rubber. Once I got the first screw in, all subsequent holes lined up. I moved down the line pulling the rubber tight, screwing the next hole. I left the rubber long on each end. Formed the trim and rubber over the angled wood part and screwed in to the wood with wood screws and finish washers. Took about 4 hours total, but some of that was waiting for the epoxy to dry, and a lot of head scratching.
I decided on screws, and not rivets, because if I ever have to do this again, it will be easier to get the screws out. I think the rubber washers on the screws will provide enough weather protection, for that area. The original rivets didn’t have anything protecting them and the water damaged ends was more a function of poor weatherproofing and using the wrong fastener.
I had been dreading this for a couple years. All in all, not as bad as I thought it was going to be. I appreciate the input.