I'm still debating how I'm going to go about the transom fix. To get a better look of what was under the deck, I unscrewed the CC and gas tank cover. The guy before me replaced the tank and hoses but used a quite a bit of junk from Lowes (treated 4x4s, great stuff, zinc plated shelf brackets and screws, and to round it out, a door mat under the tank).
The deck seems surprisingly solid considering all of the holes from the CC and the two holes for wiring chases that have exposed the core.
I'm surprised how light they made the CC. I thought it'd be a good place to cut down some weight while I'm in there sectioning out 6 or so inches but it uses less plywood core than I expected.