You really should still cut holes in the deck. You can re-glue the same pieces back in with thickened epoxy if you don't want ports.
Think about using g-10 or layup a panel yourself. Aluminum and plywood are a pretty bad solution.

Now that you have cut away the outer skin of the transom, you need to wrap the new glass job around the sides and top. You can remove the top lip of the transom and glass over that corner. It may be illegal to remove that lip, but you can put a fake one back if there are complaints. It doesn't do anything toward holding the rudder in place. You should glass the inside the same way overlapping to the sides and deck of the inside of the hulls.

If you use thru bolts and washers on the inside, they can be accessed thru your hole in the deck. If you seal that hole up, the job better be solid and not in need of later fine tuning, unless you make provisions. You can put threads in g-10 if you don't go the nut and washer route.
hope this helps.