I did get the seats and carpet out, let me know if one of you wants the plush green astro turf I took out. The seats were screwed to a strip of plywood that was glassed to the deck, It looks like a sacrificial strip to keep water from getting below the deck fiberglass. Seems like Jay did that on his sea ray helm seats.
I also drilled about a dozen places on the transom. Looks good for the most part other than a couple of areas at the bottom right around the drain holes. I'll poke around on it a little more, but I might just reuse it. Assuming the key hole is the same for an alpha, if not it might make sense to tear it out and re-do it.
For some reason the deck has a lot of "lumps" in it. I'm not sure if it is due to the deck failure and it has just conformed to the trailer or if the upper skin and main hull have de-laminated due to the rotten plywood. The rails and cross members on the trailer are all flat, not bent in the middle like a v-hull trailer. I think that I am going to leave the boat on the trailer, seems like it would be a stable platform to rebuild the hull off of. If necessary, it should be a good surface to support hull braces. I think I will also level it, then shoot some dimensions from the trailer to the hull with the laser to try to figure out what is out of whack with the lumpy floor.