I guess I must not have explained myself very well. In the photo, there is a yellow circle around a "hole". There is one on each side of my transom area. This hole is where I cut away top engine deck back when I started my engine relo. Now, (years later) I have designed and fabbed a new transom area. There is a bulkhead/rear seat back which you can see in the photos. There is also a hinged lid which you can see in the photo on the left.
Now all I have left to do is fill in the openings on either side with glass. I just don't know how to do this because I'm not thinking like a guy in the prototype department of a boat manufacturer. One thought I had was to somehow plug the holes with foam, then shape the foam to blend in with the contours of the hull deck. Then I would have to figure out how to shave the surface of the foam down below the final surface so that I could add cloth and resin back to come up to the surface and feather into the surrounding hull deck glass.
I guess this job is kind of like trying to re-glass the intake opening for the pump. If you took out the pump intake you would have a (simple) hole in the bottom of the hull. If you wanted to fill this opening, (b4 cutting a new hole), how would you do it? In my case, the shape of the opening is much more complicated than the intake hole example...