There are colorants one can add to epoxy, though I have no experience with them. I have had good luck, however, with just painting over minor blemishes to match the rest of the wood. Of course, you have to mix the paint carefully, but on a previously epoxied surface, you can start over any number of times. Epoxy and fiberglass over the hull, and no one is the wiser. Maybe it can work for you?
Good luck!