The High Frequency that starts the plasma torch is basically a lightning bolt, and it will/can couple through the grounds, motor leads, motor frames, gear rack, PC and LCD Screen cases, joysticks, limit switches, and any thing else connected to the system.
After you ground and shield everything, you may still toast Steppers and an occasional PC or two.
The hobby grade of CNC's were not designed for a High Noise (Electrical) environment.
It reminds me of building a boat out of screen mesh...You can plug all the holes to make it float but is it worth it?
Noise immunity is designed into the pc boards and is a fundamental part of the initial design in Industrial grade equipment. It costs money and so is left out of the hobby grade stuff.
The safest and maybe cheapest fix is to get rid of the cheap plasma and get a non High Frequency Start unit. Of course I will recommend a Hypertherm PowerMax unit (I used to work for them and still bleed black).
Good Luck,
Alan Bradford
www.plasmatechnologies.com