I was just looking through this again hoping there would be more pics or some updates....
What are you going to do to make sure its sealed up and water tight? I would steel flex the inside and out!
A few more thoughts....
I would also cut the Transom out of two laminated pieces of 3/4 plywood that has been screwed and glued together, encapsulated in fiberglass resin then sandwiched between aluminum. Probably use a piece of 1/8 on the outside of the transom and one on the wood for the inside, then cap it with another piece of aluminum. Or just get a section bent to fit right over that goes all the way to the floor on the inside and most of the way down on the outside. All one piece.
I don't claim to have half your skills. Im just thinkin out loud. Your doing great keep it up, and keep us posted.