Hello lost soul,
Congratulations on having the energy and ambition to start such a project. RE: the material - consider these ideas if you have not already......(1) use the same type of material that you removed (not a revolutionary idea there!) (2) Use your choice of materials based on the amount of space you have to accommodate the new material (new materials may be thicker or thinner than the original) (3) Epoxied in place the replacement material will surely last many, many years. In the two repairs we have made we used plywood for a large area of the foredeck of a small boat and we used epoxy and fiberglas for a small repair on a larger boat.
After you make the choice and complete the install you can hide/disguise/blend in the repair by painting the deck area. We have done that several times and were completely satisfied with the result. In our case we used Interlux paint and added the microbubbles for non-skid properties. Eileen, my wife and general life coach, rolled the paint after taping the edges of the area and then created a finished look by dabbing the wet paint with a sponge to blend the entire look. Best Wishes!
BTW: I just remembered this. When repairing a loose fitting hatch on a powerboat I found that using a large piece of plywood caused the hatch cover to warp. Therefore, the balsa coring material or several smaller pieces of plywood might be far more satisfactory than one large piece of plywood.