I've heard about the calibration issue ,but have never used it. Just do the math to get your steps/unit, make a cut and measure. If it's off, do the math and enter the correct number. Done.
Sounds like noise is triggering the E-Stop. A band aid fix is to increase the debounce in general config. Try a value of 2000 to start.
As for Mach3 not stopping, get a switch with another set of contacts and wire it to an input pin to mach3, so it knows to stop.
What are you controlling your spindle with? The pulse rate shouldn't vary much at all. If it does, you'll notice it in your steppers too.