I too replaced the perished seal on the rear hatch of my Mark 2 but could not get a seal to the 5 inch water-gauge standard in the Wayfarer Book.
I took a radical step and decided to put the gasket on the hatch instead of the hull. First I laid a straight edge over the top of the hatch coaming to establish that it was flat and in-plane (ie not twisted), that was ok. then I checked that the hatch was similarly flat, that was ok too.
Of course the hatch cover is cambered so if I want to match the coaming top to the gasket I had to create a flat flange inside the cover, which I did by sticking a 20mm wide piece of polyurethane foam all around inside, then made a jig to sand it back so that the flange was parallel with the hatch edge. The pictures explain better than the words. Some woven cloth and epoxy resin made a hard skin which was filled with microbaloons and epoxy resin (a mixture that a mate of mine tells me is technically known as bog), which is easily sanded fair (using that jig again). Finally I obtained some 9mm thick self-adhesive neoprene foam that I stuck onto the flange inside the hatch cover to create the seal. The pictures are not in the correct order, sorry, some things are too hard.
A little bit of rubbing was necessary to get the coaming edge true. I used smoke pellets in the tank whilie I pressurized the chamber by blowing into a pipe to find out where the leaks were, followed by judicious rubbing down (and occasional filling) to get a good seal. Unfortunately I do not have a photograph with the neoprene stuck on (use bicycle repair adhesive to seal the corners), but if anyone is interested I can take a shot next time I am at the club.