Used clear contact paper on the inside of the hull, laid down foam weather stripping, built up each side of the stripping and laid several layers of glass over it, removed the layup, removed the weather stripping, reglued the layup onto the underside of the deck. Trimmed the layup from the top side and installed new weather stripping into the grove left by the previous tape.

Randy-
I can't remember where I've seen that before, but it sounds like a good system for building a 'ledge' to hold a foam seal strip. The wooden hatch lid is flush with the deck (since it's cut from the deck itself). So after the layup is removed from the 'form' - the underside of the deck- would be the time to cut out the 'hatch cover' shape. And, if you were going to add a 'deck beam' to keep the shape of the hatch cover, it would be glued on (glassed on?) before cutting the cover free from the deck.
I'd use a half-thickness foam strip for the layup stage. Also, I'd glue a cord or wood strip 'ridge' to the cover to push into the foam seal.
It still surprises me how many layers of glass are needed to make a 'stiff' layup, so I'd recommend erring on the heavy side. You might want to make up a few test samples. Buying a couple of yards of 10 oz cloth if you have a nearby supplier might help.

Be sure to drill breather holes in your bulkheads; it will help to keep your hatches from leaking.