Just something to think about, if you use Epoxy based products, you won't have good luck laminating with polyester/vinylester products over the top of the epoxy stuff.
Anyhow, do do the work, make a good template, after all the bad wood is gone, test fit the template a couple of times to make sure it works. Cut 2 pieces from your plywood using the template. Make sure it matches up well, and test fit each piece against the transom. Then cut 2 pieces of mat with the template to match the wood pieces. When the inside of the transom is prepped (40-80 grit sanded) and cleaned with acetone, wait for the acetone to evaporate completely, then lay up the first layer of mat, the first layer of wood, clamp it all down to get out the air bubbles, and let it kick off. Then the second layer of mat, the second layer of wood, repeat the clamping, and let it kick off. After that, cover the entire thing with 2 layers of mat, a layer of cloth, and a layer of mat again. Something to note, The cloth needs to be laminated in between layers of mat to have any effect. It is kind of like the rebar in your repair and unless there is concrete on both sides of it, you might as well not have it there to begin with. That being said, I would laminate the first layer of mat, make sure it is nice and flat and rolled out good so there aren't any huge resin bumps that will continue to build through your lamination; then let it kick off. Then mix enough resin to do the second layer of mat, the later of cloth and the last layer of mat. After you're done just remember that any holes that are drilled through the wood need to be sealed with resin before anythign is installed, and then also sealed externally with 5200 or the like.
Chris
