Without pics no one can tell you exactly why your driveline is vibrating, but I'm guessing it's because of lack of support. Make sure the stuffing tube is epoxied in good. For the rest of your stuffing tube that in inside your hull, cut a piece of fiberglass cloth and drape it over it, allowing the ends to run accoss the inside of your hull. Then either use a thin layer of epoxy to soak into the cloth, or use thin CA and the cloth will wick it up. What ever one you do, when it dries it will be very stiff and should eliminate the driveshaft vibrations.

It would also be a good idea to do the same with your motor mount.