M00 - Program stop. You can insert that into your G-code in the spot where you'd like to stop. I'd recommend doing it after a z-retract of some sort or, you can write in a simple z-retract line on your own. If you stop the spindle manually, remember to turn it back on again before you hit cycle start!
Pressing the stop button on Mach causes lost steps if the machine is running at any reasonable speed because Mach 3 just stops the pulse stream, no deceleration. If you want to stop in the middle of a program in an un-planned sort of way, Feed Hold is what you want to use. It will stop the machine following the acceleration limits set in the motor tuning screen. Cycle start will pick up where you left off.
BTW as you can probably guess, the pucker factor is quite high the first time you feed hold, move the spindle out of the way and then continue....just don't forget to turn on the spindle! One day when I walked into the lab and found that my fret slot bit had broken about half way through a fretboard. I found the appropriate line of code, put in a new bit, fired up the spindle and hit "run from here". I about crapped myself when the machine shot over and dropped into the fret slot at 400ipm+ but, everything worked out fine. Take your time, double check.
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