Ever try putting together one of those furniture kits where the diagrams make no sense? I had a chair once where all the side pieces looked identical until you tried to screw them in wrong. Ended up putting little bits of tape on the ends that matched up, like a dumb puzzle. Saved me from having to take the whole thing apart twice. Guess that's the same kind of logic, just with wood and pencil marks.
Wait, you had to take the whole thing apart twice? @cameron_price, that's the real nightmare. I'd lose my mind. The tape idea is smart though, way better than my system of just getting angry at the pieces.