yeah, it's hard to completely describe with words or understand from description - but I'll try to explain how my 89 was...

The floor width was such that the top of the floor went full width, port to starboard, just shy of touching the hull wall and was tabbed to the hull with glass around the entire perimeter. The bottom of the vertical inner wall of the top cap sat right at the top of the floor. There was a ~2"x2" piece of wood glassed into the top of the floor/hull joint (behind the inner wall of the top cap) that ran along the length from the aft end of the cap liner wall to about where the observer and driver seats mount. The top cap is screwed through the cap liner wall into the 2x2 backer.

I screwed up & ended up with the floor too high at the rear so that the cap wouldn't sit down on the hull because of interference of the cap liner wall with the floor. I just trimmed the bottom of the cap liner wall ~1/4-1/2" so that the cap would shoebox on the hull. Hope this helps, but let us know...