When I put my shell back on, I had holes that didn't line up as well, tried a dozen different things to try and get the frame to flex so that the the holes would work, but ended up giving up and drilling new holes. I have a '73, so the rivet line was all covered by a piece of trim anyway, so I didn't have to worry about the way it ended up looking. I also didn't have such a mismatch that I missed the entire channel. Anyway, I assume you have already tried things like messing with the leveling of the frame in order to get things to line up a little better.
So how to fill the existing holes....What would be ideal would be if you could install a blind (or "pop") rivet that can be counter-sunk so that you could minimize the appearance of the "plugs." I am not sure whether such a thing exists. If you could slip a piece of 1/8" steel between that row of holes and the plywood (to searve as a permanent anvil), then you might be able to buck in some counter-sunk solid rivets from the outside.
Good luck!
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