Hood,
Tried that and it doesn't work. It acts almost like the TB6560. After I posted I tried lying by changing the pin numbers with no luck. That is, I pushed the page down key and noted which stepper moved and then assigned that pin number to the Z axis . . . nothing changed. The pins for the Gecko 540 are very easy to remember, 2&3, 4&5, 6&7, and 8&9. It works fine in Mill mode. We plasma has not worked from the start but I did not pay much attention thinking it was in the setup.
I just used mill mode for the learning curve during which time I thought I would add a THC to the project. Not sure that I really need a THC but I was amused by a rotary axis add-in that came with it. The THC arrived by the time the table was ready to go. The THC came with its own setup parameters and it was never necessary to perfect the Mach Plasma mode.
When the time came to execute the test protocol for plasma portion of the THC a board in its controller got fried. However, before that and now the THC motion control and its setup worked just fine. The THC used the aforementioned pins, 2&3 and so on.
When I set the Plasma mode using the same protocol as in Mach Mill and the THC it does not work. It acts like it is locked and the pin values do not change anything. I found a post with the exact issue but I did not see an answer.