With it installed back on the car now, the gaps now looks perfect. I was originally targeting 3/16" wider, but it was very difficult and I settled on 1/8" wider, and it turned out perfect so I'm glad I quit while I was ahead.
Pictured below is the end result (both side look like this now). I'm not sure I have any "before" photo, but I can tell you before I fixed this that the gaps jumped out on both sides as seeming misaligned.
I also wanted to bow the rear edge of the clamshell upwards a bit more to make it better match the rear decklid profile of the fiberglass Aerokit 1 rear decklid, and it seemed I managed to make a noticeable improvement there also. As I bent the clamshell wider, I noticed its front edge would get tend to get pulled a bit downwards/flatter, while the rear would tend to arch up a bit more.
I can't describe why this was necessary - maybe as evidenced by the "racking", the clamshell originally got bent by previous owner somehow? (I can only guess on its previous history, but the 10mm fastening nuts securing clamshell to hinges had definitely been tampered with, so someone was in there before me.)
One more potential explanation is that wear in the clamshell sliders is a factor. (I noticed there was a bit of in-out play in my sliders on both sides - they were also pretty dry before I cleaned and lubed them!) Maybe if the two sliders were "new and tight" without play, they would have kept the clamshell ends spread out a bit more, even when the width of the clamshell wasn't totally perfect. I imagine relying on the sliders to keep the clamshell ends spread apart adequately, however, (e.g., it that's how the car was originally built), could dramatically accelerate wear on the sliders.
Before I got to it, the clamshell hinge mechanism was badly in need of lubrication, and now after lubricating it and fixing the racking of the clamshell piece, the top mechanism seems to be working very smoothly!
(There seems to no longer be a "popping" noise associated with initial clamshell opening/closing that I remember used to be there, and it seems the top motor is laboring a bit less.)