Capt Dwight,
Welcome to CSC. I noticed from your web site that you're in Chatham. That is a great area to fish and there is quite a collection of classic SCs too

. I'll let some of the experts speak to your transom issue, but as far as a windshield goes, try
Palco Plastics in Whitman. There may be a more local shop on the Cape, but Palco does a nice job.
For the aft deckplate, I'm guessing you mean the rectangular hatch in the splashwell. If so, you should try a watertight hatch from
Bomar.