How long was the tape on the boat? If it was for an extended period of time (weeks/months), the wood may have "tanned" or "bleached" slightly where it wasn't covered by the tape, leading to a difference in color. If that's the case, it should even out over time as the boat is exposed to the sun.

Removing the residue is easy with lacquer thinner. Unlike acetone, it can't hurt the epoxy. One thing I would NOT do is to try to sand off tape residue, as that will spread it around and drive it into the surface scratches created by the sandpaper.