A spirit level is a good way to check for alignment. Checking the top of the light box is useless. It doesn't need to be perfectly level, and often isn't. Things to check are:
- The baseboard. This doesn't need to be level, but you must be able to determine just how much off level it is. Check it side to side, front to back, and along both diagonals. Everything else must be parallel to the baseboard.
- The lens board. This needs to be parallel to the baseboard.
- The negative carrier. This needs to be parallel to the baseboard and the lens board. Check it the same way, side to side, front to back, and both diagonals.
Fun, huh? It's not as bad as it sounds.