Final thoughts and tips:
Until you remove the ports and disassemble the frames you don't really know what you have, or what a previous owner or contractor has done. In my case not knowing how the 323 was originally assembled I had thought that the deck and liner port opening had been fiber-glassed together at the factory. Some parts of the openings looked like Richard's pictures with a gap between the deck and liner, while others were a single layer of fiberglass. When I measured the frame gap, deck to liner opening, it was just over 1/2", but where I only had a single layer of fiberglass it only measured .300", so no seal pressure when the frame was completely tightened. The reality was that in a previous attempt to fix the leaking ports someone had bonded the deck and liner together with a silicone sealant and clamped them together alone the ends and corners. It was so tight that you could not see a seam. I found a small gap mid-opening and hammered a putty knife in between the desk and liner. Once separated from one-in-other the gap returned, and was a miraculous 1/2" just like the designer originally planned.
Tip: Use an oscillating multi-tool with the triangular Velcro sanding head, cut a piece of scotch bright to fit. Soak with MEK and use to clean the deck side sealing area. Removes just about everything and leaves a completely clean surface for the sealant.
Tip: Get new frame screws, even the least little bit of round over makes it much more difficult. Screws are #8 x 1/2" sheet metal, available with black heads. At the frame ends I used 5/8" for a little bit longer grip and pull.
Tip: Hand start the screws, if you find the original threads life is much easier. If you are going to use Butyl for your frame to deck sealant... tighten, let sit for a day or two, retighten, let sit, etc. etc.
Tip: (Maybe the most important) If you are doing this work when it is 95 degrees in the shade and 98% RH. Put a dry t-shirt in the drink cooler, at the end of the day strip off the soaked one and put on the now cool and dry one. It is almost as good as taking a shower. Sit in the cockpit, drink in hand and admire your work.
So far: No runs, no drips, on errors. Getting closer to a dry boat everyday, now on to the opening ports.