How do I figure out the effective diameter of the ruby probe tip? No such number was provided to me. So I used the 0.118" figure given in the manual; it also happens to be the diameter given by my indicator. So I assume it is the right number. Yet every part I have made using this probe is off by 0.04X".

What number do I put into the mach3 software, and where? Tool 99 in the tool table?

I have already completed the alignment procedure. After 6 iterations I got it down to 0 turns on each of the three screws.