A depth mike will not give an indication of whether or not the flange is square to the film plane. As I mentioned above, support the camera at the filmplane on a surface plate and use a dial indicator to measure paralellism. The depth mike will be good for measuring the correct distance from flange to plane.
Originally Posted by Nicholas Lindan
To the op: if the shims for the screen weren't disturbed, leave them be for now. The first step is to get the flange parrallel to, and the correct distance from, the filmplane. Second step is to get focus on the the screen to coincide with the focus on the filmplane.