Anthonya is correct. It is stylus rake angle you have to pay attention to. There is no program to measure this. It has to be done by site. Contact cement bright white paper to a small wood block and from one edge draw a crisp 92 degree line. You place the block on the turntable behind the stylus so you can see past the stylus to the line. You want to get it as close to the stylus as you can. Then you raise and lower the back of the arm until you match angles. Some stylus profiles make it very easy. Gyger S, Soundsmith's OLC and I believe Ortofon's replicant stylus all have an oncoming face that should be exactly 90 degrees to the surface of the record. This puts the contact patches at 92 degrees.
You can get the microscope very close to the stylus if you plant the stylus right at the beginning of the record. The problem then is the record lip gets in the way. My own solution to that problem was to take a hand plane and shave the lip down to flat on my old set up record. My turntable's platter was the same diameter as the record. If your platter is much larger then you are in trouble again because you can't get the microscope close enough. I might have a problem with my new table because the vacuum lip might get in the way.
The most important issue is stabilizing the microscope in the horizontal position at the edge of the platter which might take some creative thinking. You can take a wood block of the right thickness and velcro the microscope to it as an example.
