[NOTHING ELSE MATTERS]

First off you shouldn't had cut the outer skin of the transom. What you should of done was cut about two feet the cap, unscrew some of the rub rail and remove tha section of the cap, then remove the inner layer of the glass and ALL the plywood, by doing that you still have the skin outside to use as a guide(our boats have bowed transoms, not straight), and also you could cut the floor about 2-3 feet in to tie the new plywood to the stringers(most likely the stringers back there are rotted too.

Now, what you have to do is remove the rest of the glass from the inside(at the last pic. shows that you have about a foot left), remove the rest of the rotted plywood and i think you still have to cut the cap away anyway. Sure looks like a big mess now but when you done is gonna be good for another 30 years or so. Use marine plywood, do be cheap on that, otherwise you gonna regret it later. Good luck and keep the pics coming.