---

To fill old holes it is probably easier to raise the bow than the stern. So, raise the bow as much as possible [the more the better].
Tape a piece of plastic trash bag, saran wrap ect. to outside of transom and whatever you want to protect splash well. Put an epoxy resin that has been mixed in a suitable container to squeeze it accurately in the splash well side of the hole. I use old saline bottles with the tip cut a little bigger. Fill the whole thing. Since you have not made the hull verticle, you will need to finish the splash well side with some thickened resin, or some other epoxy putty.

When you are drilling new holes it will give you a good read on any moisture in the plywood of the transom, if any.