With the mirror system, you really should use front surface mirrors so the glass doesn't get in the way. I put 2 sets of 4 tape arrows around the hole. This will aid you in seeing the misalignment. Also, when doing the negative stage I would remove the lens and bounce light off the mirror on the base board. What you are looking for is the effect you might see while sitting in a old time barber shop chair with a mirror in front of you and one behind you. If the stage is out of alignment, then those arrows will start out in the center and then veer off in the direction of the misalignment. If you are ok then the arrows will go straight out untill you cannot see them anymore. It is a lot easier to do than explain, really.