Did you try running the code at half feed like I suggested.? Just becuase the Axis Jog at Rapid speed ok doesn't mean they will work when running the G-code, it's a common problem when Mach is overly tuned.

Now I ounce had an 10x5 Machine I built and while running my test G-code cutting air which is basicly 1000's of moves covering all the cutting area would E-stop at exactly the same point in the code and location on the machine.? Only while cutting AIR did it do this. I could cut a Job in that location with no problems and had surfaced the bed etc without any issues.
All logic told me it was a software/Code problem because it was repeatable and exactly at the same point in the Code.

After 3 days tearing my last strand of hair out and going over the PC and machine top to bottom I found the issue.! . . . It was a poorly crimmped ferrel which at that exact location on the machine, which happened to be in the middle of the gantry and roughly half way down the machine, must have caused an harmonic vibration which was just enough to trigger the E-stop.
Now the Controller was a CSlabs IP-S which are very fast reacting to input signals which is a good thing, this might not have hppened on lesser controllers if the wire didn't lossen any more but more likely it would as it worked lose over time much further down the road.

So check your wiring very carefully it could be something silly like this.?