PonyBoy, In 2007, I did much the same as what you're doing, except my transom was useable. I subsequently sold the boat to a very happy walleye fisherman here in NW Michigan. I replaced the floatation and floor, salvaged and reconstructed the center console, left the transom alone after probing with an ice pick, and caught many king salmon on Lake Michigan with it. I used 5/8" exterior grade plywood painted heavily with Kilz sealer primer. I did the same on my 19' Great Lakes Special (SeaNymph). In retrospect, I wish I had used 3/4" marine plywood in both, but sealed 5/8" exterior will probably outlast me. The 3/4" marine would have added needed weight to the Mariner. Instead of carpet, because I didn't want to get hooks caught in the loops and didn't want to scrub off fish blood, I used marine vinyl sheet carpet on the Mariner, and heavy gauge roof membrane on the SeaNymph. Both were good decisions. Be sure to take time to replace all the floatation cells with fresh, spray in waterproof foam. Spray every crevice. It will be a safer boat, and it will support your floor well.
Where are you with this project now?