I think you're on the right track with the foam bulkhead. You wouldn't need to be as precise -- just cut it a bit oversized, wedge it in place, and caulk it. Caulking thru the little day hatch will be the fun part...

I think you will want an easier-to-remove-and-install day hatch, though. Trying to screw in your hatch cover behind you in rough seas could be too much trouble. The picture here is from Betsie Bay Kayak's page -- they use Beckson pry-out hatches on their production stitch-n-glue kayaks. They put a small black knob on them to make them easier to remove. A loop of cord coming up thru the hatch cover would work as well. It's hard to see in this picture, but BBK used to also put 2 little white toggles on either side for extra security. They help ensure that the lid stays on, and swing out of the way to open the hatch. I don't believe that BBK uses these anymore -- they stay in place without them. The hatch lid has an O-ring that seals water out and also provides the press-fit that keeps the lid in place. And they stay in place well. They once had a customer's windshield break when the lid blew off the upside-down kayak on their roof rack in the hot sun. I think they have since vented their bulkheads. BBK has also added the option of mounting these hatches under the deck. The cutout from the deck is glued to the hatch lid, and a little pull loop is all that is seen on the deck.

Dean