I would not use 5200 to bond the two pieces of plywood together. That stuff can take a really long time to cure and there are better adhesives for the job. PL premium would work, but after using it you'll need to wait at least 72 hours as it cures and offgasses. A better choice would be either resin and fiberglass, or Titebond III. Titebond is probably the easiest (and least expensive) to use, and it cures/dries overnight. When dried, it is at least as resistant to water as the glue that holds together the plies in exterior plywood, meaning the plywood glue will fail before the Titebond if it gets wet.
I agree with the suggestion to use peanut butter/thickened resin to bond the transom to the hull. As soon as it cures, you can continue glassing. If you use PL Premium, which also would work, you again have to wait another 72 hours (and probably longer if it's cool where you're working.). If you try glassing too soon over stuff that was adhered with PL premium, you're liable to get bubbles in your fiberglass.