On that era prostar, I've never really liked where the coaming panels 'bumps' up to the angled portion that accepts the end of the windshield (pic in post 1). I always assumed it covered up something in the top cap behind it. On the Tristars, the coaming panel goes straight across along the top edge.
This probably goes without saying, but please don't drill thru the side of the hull when anchoring the "3-inch shelf mounted above the midline of the hull".
I was trying to envision what you had in mind there.
Interested to see what you come up with as my coaming panels (and interior in general) are getting close to needing replacement. I've thought about enlarging the current openings on mine and reusing the vinyl, but they remain as-is for now.
When I replaced my carpet, I relocated the stern light pole and mounts from where it was mounted on the floor between the coaming panel and the sidewall, to the inside face on the bottom of the coaming panel. Just gets it out of the way a little bit more.