There are hundreds of thousands of high frequency start plasma systems operating on cnc cutting machines worldwide. All industrial plasma systems from about 120 amps and above are high frequency start. Industrial cnc machines and their associated controls and electronics have extensive filtering, grounding, and input/output optical isolation that makes them work reliably with a high frequency start plasma. Industrial high frequency start plasma systems use high frequency to start a pilot arc, which allows transfer to the plate from a reasonable distance...3/16" to as much as 3/4" on large systems. This arc transfer distance allows the blowback molten metal to miss the front end of the torch...preventing damage to the nozzle.
The plasma system that you have is a high frequency start WITHOUT pilot arc.....meaning the nozzle must get very close to the plate to transfer the arc. This works acceptably in hand cutting applications as you can tip the torch to cause the molten metal to miss from hitting the exposed nozzle. In mechanized cutting....you will have trouble getting this type of torch to repeatedly pierce anything thicker than about 1/8" without damaging the nozzle...which will affect cut quality. Further...if the material has some dirt or rust on the top surface...often you will have to scratch the nozzle on the material to get it to start the arc.....again, not the best process for mechanized cutting.
Back to the high frequency noise...you did not say what you built for a machine. If it uses a standard PC for control, uses stepper motors and unshielded cables, unfiltered electronics....you likely will have issues with electrical noise interference. You can solve the issues buy adding filters, optical isolation, shielded cables, ground rod......but you likely will burn up a few system components in the process. It may be cheaper to buy a modern plasma with a non high frequency (blowback) start.
I'm not trying to discourage you....you may very well be able to make it work...a few have! There just is no exact science to solving high frequency caused electrical noise interference issues on homebuilt machines. You may want to consult with the supplier of the components used in your build..they may have some advice.
Jim Colt Hypertherm