I recently did a transom job with a clearence issue like that. My supervisor has an extended shaft straight die grinder that helped a lot, along with a few carbide bits and a stone ball. Later, I had closed the gap even more with glass, and had to come up with something else. I taped a stir stick to a sawzall blade, and cut a piece of psa 36 grit sand paper to fit it. It was a bit slow, but worked well. Longer blades will let you put some pressure on and flex them.
As for the sidewalls, just gel would probably be best. If you use the foam, could you set up a blower on a timer somehow to dry it out? Even just a tiny box fan left in overnight would work.
