3/8" wholes in transom - how would you fix?

[McGillicuddy]

Option 1 is the better way. After the bolts come out you might spray down the holes with some alcohol to dry the wood some. I cut dowels to 1-3/8", soak the dowels in "neat" epoxy, tape the downhill side, fill the hole with thickened epoxy then ease the plug in, slowly displacing the putty so the walls of the hole are saturated with epoxy too.