Update!
Got the outside of the transom smoothed out, still minor repairs and some fairing to do though.
I used Loctite PL to bond the 3 sheets of 1/2 inch together, I put several hundred pounds on it for 48 hours and had great results, even spread no air bubbles.
Got the center transom epoxied into place (I used West Marine, 105, 205, 404, and bit of loose fiberglass, more so on the loose strands at the bottom where a fill was necessary), got a coating on the back and sides tacky then used a ton of epoxy (25-30 pumps) to get the transom stuck to the hull and fill in the gaps at the bottom/fillet the sides. Gotta got back, smooth it out, tab it in, then cover it in biaxial 17oz (no matting). When that's all set I'll be adding a half inch of "extra" transom from the center extending to the sides, for some extra support but mostly so the towing eyes are strong for tubing on the water, and road trips.
I'm at a standstill with my decision on paint. I was originally going to use SM-1000 but it appears it'll be quite difficult to work with. So then I decided on Interlux Brightside, and again withdrew that decision. Now I'm thinking I'll either do the whole bottom hull (and top cap, different color) with tractor paint (as recommended by WoodOnGlass) OR do a below the waterline Interlux VC performance Epoxy then tractor paint the hull above the waterline. I'm mostly looking for what will come out best and last, I don't mind difficult work but I know some of these paints require very specific details and I want to assure a perfect, strong, finish.
Look into the PreVal Paint system works REALLY well.
That looks AWESOME, but I think I'm going to end up just buying a HPLV setup for cheap for this entire job, I already have a compressor.