What lathe is it?

I can't understand the issue with "calibrating" the axes. It's just a matter of doing a straightforward calculation and typing the steps/unit into a Mach3 text box.

I'm not familiar with the "100 kHz breakout board" but I assume that it comes with a Mach3 plugin for the USB port? Do you have this? Many of the USB controller from the Far East have a poor reputation for the quality of the USB implementation. I use CNCDrive UC100s and they work perfectly for me. Does the one you have support threading and probing? These have to be done in the motion controller - threading is mandatory for a lathe to be much use and probing is useful for tool setting. Mach3 is fine for threading on a larger lathe with plenty of spindle power and inertia.