The whole problem was after I put the bottom sheets of plywood on, I added another piece in the middle where the generator sat. I didn't get the pieced sealed good enough and I had water infiltration from the inside of the boat out after water sat in the bilge area. Where you see the paint peeling was a bad epoxy mix. I thought we got the gooey stuff off, but once a little bit of moisture hit it the problem grew. The transom has held up great and I don't think I'll worry about that. I am going to add some keels to the bottom to help with the steering. I don't enjoy running straight down the river with the boat pointed at the shoreline, especially when another boat is headed straight towards me! I think I'm going to change the seating arrangement and try to do away with the footwell. I've got a couple of stress cracks in the top deck this should fix.
By the way, I'm thinking about starting a small business on the side building aluminum jons. Think there's a market out there? They'd be completely custom ordered with fans and decks if interested. I could only handle a few every winter.