I can't remember where in Mach3, because mine had been preset by someone else, but I believe it has some internal functions for calibrating an axis.
If you used 4000, just measure how far it moves when commanded to move 1.0000".
If you measured say 1.2" then you need 4000 * (1.2000/1.0000)
Trying just other big numbers will other big errors.
Remember that on the lathe you want the x-axis to move 0.5000" for 1.0000" on the DRO, unless you like measuring in radius.
Z ax-is 1:1. Z towards the chuck becomes more negative.
X towards small diameter becomes more negative.