Ok I have the machine working now, having configured it like tripleblack suggested. Thank you very much for that. Next bridge to cross is that as soon as the plasma fires it causes a e-stop. Even when I don't command the G540 to fire the plasma it sets it off when I turn on the torch manually. My plasma cutter does have HF start and I have tried shielding my cables as best possible. Any suggestions?
That's most likely because the Chinese plasma you're using (1) has HF arc start and (2) emits tons a HF noise. As soon as the torch fires, the surge of HF noise on the system causes the eStop. Increasing debounce may or may not help. We tried setting up one of those machines and went all the way to 10000 on debounce with no luck. Turned out that even just running the plasma 50 feet away by hand and not even attached to the CNC table would still trigger an eStop on the table.
I've heard of some people using these machines with some degree of success. The first thing you want to do is make sure your grounding in by the book. Shielded cables grounded properly and everything, even the PC, grounded through a ground rod driven as deep into the ground as you can get it.
If you turn off ALL inputs (IE: limits, home and estop) it may work. It didn't in our case as even on a properly grounded system, there was enough HF noise to interfere with the motor signals.