You could drill the holes oversize and a place the boat on its side with one hole level. Block the other hole with plastic, or something that epoxy will not stick to and pour full with some chopped glass added. Place a dowel (1/2") in the holes while the epoxy is wet. When hard, drill out the dowel.

Might want to use wet towels to take some of the heat from the pour or submerse if possible while pouring, the bottom hole would have to be really sealed though. Good luck in the end!