You are trying to do several different things, so one strategy probably doesn't work for the whole project. It's also nice to try and find the solution that is the least expensive and least work.
To make the footwell shallower, to my mind it seems like new steel is the best choice. This will be the strongest and most trouble free way to deal with a horizontal surface in which wood and steel will not get along. The footwell is likely a simple rectangular shape. You could make a template from cardboard and cut the steel with thin cutoff disc in a grinder. It will need a bit of steel angle stock under it to make it stiff, you can probably just copy the underside of the original cockpit sole.
It sounds like your original thought was to build up the cockpit benches with wood to give them more height so that you could have a deeper lip to the locker in which you could implement the double coamings for the hatch. I'll wait for pictures and for others to comment, but the effort to build up the benches in a lasting way might be more work than an alternate locker lid. I once made a set of wood cockpit lids for a Hurley 20. I used cedar and fiberglass to make lids that had an inset gasket. It's not as good a solution for ultimate watertightness, but they were very strong. If you're just coastal sailing this would be quick, cost effective and safe.
Annie's idea of closing the entire cockpit gives the ultimate in watertightness, if it can be made to work in terms of space, access, comfort. Here again, a sheet of steel makes the most sense for strength, maintenance, cost.
I took on rebuilding an aluminum boat a few years ago without much metalworking experience before that. Boaters think a lot about wood and epoxy because they are everywhere, but metalwork is just different, no harder. I prefer the feel of wood and find it more pleasurable to work with, but for the outside of a boat there are good reasons including strength, durability and maintenance to stick with the metal you already have.
With some pictures, I'm sure others will post even better ideas.