Well you have a worthy project. You need to get the deck off to put a transom in so you need to decide whether to remove the whole deck or just the back section. Once you get that done, you need to get the rot out. That is a long itchy process. The stringers and core are bound to be at least partially bad. You have to decide what materials you are going to use. Balsa, plywood or synthetic (Coosaboard etc.) Polyester resin or epoxy.
Time to get grinding! Good luck!