Nicholas,
here is how I made a set of new cockpit hatches for my Johanna, back in 1999. Johanna was an owner-finished version of the Alo28, so the hatches of this boat had been glued together from thin planks. With the glue failing, all the hatches were about to fall apart, and of course leaked a lot.
On taking a closer look, I found that the hatch openings had been well made with a moulded ridge and then a groove around it to drain away water. I therefore made the hatches from plain 15mm plywood. Instead of trying to make them as tight as submarine hatches, I simply skipped fitting gaskets. Instead, I made a simple ‘drip lip’ from Sikaflex, running continuously along the edges. See diagram and photos below.
Having never seen this in use before, I tested it by laying old newspapers inside the cockpit benches (-trunks?). Paper from newspapers not only tells if it wet. It also tells if it has been wet. The result was perfectly good - dry newspapers. Maybe you can pick some ideas from this and use on your boat.
I don’t claim that this will keep out all the water each time the cockpit is filled up (how often does that happen?), but if strapped down, they should only let in a few drops now and then.
About making the foot well smaller: What about tailor-making one or two trunks which you secure in the foot-well? These will take up volume there, and in addition they will add storage space. I would of course have made them with the same sort of simple plywood lid as mentioned above.
Good luck!
Arne