Okay, after a bunch of research on the spray pockets I decided to have them filled in by a body guy I know. He has done extensive fiberglass work over his career, including building boats from scratch. He had me go to a junk yard and by a fiberglass canopy for a truck so that he could use the angle of that to match up with the boat. He glassed in ribs for strength, then covered it all up. Went back and drilled holes and sprayed in foam. Then sealed it up and shot the gel coat. It turned out better then I could have ever expected.
The guy works for ridiculously cheap, all together it cost me.....Wait for it....... 350$ including materials
Before the work shots
Here are some of the shots from the work.