Joel must have missed this, but I'll try to help. I do a lot of projects like that one, no problem.
Now, how should I wrap the decks and bulkheads, and how should I glass them to the hull sides, transom, and deck?
Looking at this picture
The first thing to do is grind off all the paint or gelcoat down to bare clean glass where the new frame meets the bottom, and the sides, and 6" out on either side. Same thing where the new deck meets the hull sides and transom. Clean it to bare glass all the way over that lip, and about 3" below the deck. Everywhere there will be glass has to be clean.
I would install the frame first. You will glue it in with epoxy thickened with wood flour, then build a filet around all the edges, inside and out. Over the filet you use 6", 12 ounce, 45/45 biax tape and glass the frame to the sole (floor) and sides, front and back.
Then you need to cut some cleats to support the deck, at the sides and along the transom. 1X2 pine is good. Mark and glue them in place. Along the top rear of the frame will also need a cleat for support the seat, glue that on too.
Coat all wood in epoxy, both sides, cleats, plywood, everything, 2 coats.
Smear plenty of glue on all the cleats and glue down the rear deck. Use the squeeze out to form filets along the sides and transom, then tape these in with biax tape. Let the tape roll over the gunwale lip and transom top. Another strip of tape along the forward seam. That edge will first need to be rounded over to about a 1/2" radius so the glass will conform.
Now you can cover the entire thing in glass cloth. I'd use 12 oz. biax cloth, some people recommend woven, but I like biax better.
The front deck will go the same way.
Bill of materials: pretty close anyway..
4.5 gallons epoxy (Marinepoxy)
5 pounds wood flour
50 yards of 12 ounce, 6", 45/45 biax tape
10 yards 12 ounce 45/45 biax cloth (50" wide) You will probably use about 7-8 but it's cheaper to buy 10.
Glassing in these frames and decks are really going to stiffen up the hull, but you can run lengths of the tape down the rolled gunwales to build them up. Patch any holes first. You could also add some foam stiffener panels on the sides if it still needs more.
I'll add a few pics that might help in a few minutes.