One of my problems is that I am using the IP/M which supports dual axis machines but does not do gantry squaring. To do that, you pay a lot more money for the IP/S. Originally, when I turned the machine on, I homed it using the standard Mach3/IP/M homing routine. X and A axes move together but you cannot guarantee that the gantry is square. So, I hit e-stop to take power off the motors, turned the A motor by hand until the LED on the proximity switch went out/came on (copying the Mach3 homing routine), then reset and rehomed again. That is OK but it was difficult to be exact, partly because when X homes it then moves the axis a short distance (1mm, I think) to move it away from the prox switch but I was never sure exactly how much to move the A axis to match.

My current system involves going into the IP/M configuration dialogue, turning off slaving, running a custom macro that homes both X and A simultaneously, and then turning slaving back on. In principle this is more accurate as you can use the "home offset" feature to make fine adjustments to the gantry position at each end to get it square and use that to repeat accurate squaring each time. But it's a clumsy process, particularly if you forget one of the dozen or so mouse clicks needed to do it.

I have other problems with my machine setup as well which I believe are due to interactions with my wireless pendant as well at the firmware/plugin level - each of the components works fine by itself and it's just that combination that gives trouble.

So, I've tried "simple but not very accurate", "accurate but fiddly", and now I want to do "quick and accurate"!