I would use 12mm or 19mm (1/2″ or 3/4″) thickness, say 100mm x 100mm. The actual material depends on what you have to hand, builders merchant marine ply can be poor quality, but if you have the proper stuff from Robbins Timber that’s ideal. If you happen to have some appropriately sized hardwood that would be ok.
Epoxy in place with a good thick mix (peanut butter consistency) after the transom has been cleaned up as best you can from the old timber/fibreglass, try to get a reasonably flat surface for the timber. The timber will need clamping while the epoxy sets.
I don’t see any point in glassing over the new timber, apart from being more work there is a danger of moisture being trapped. A coat of unthickened epoxy over the other faces will help protect the timber if the buoyancy tank tends to have water in it.
When the pintle is fitted some sealant (e.g. sikaflex 291i) on the bolt holes will keep moisture out. Some good sized washers on the bolts as well to spread the load.
Hope that helps