One of the main ways in which noise will get coupled between parts of the system is by running cables next to each other. I wanted to make everything neat by having all the cables for the spindle, motors and limit switches running through one set of drag chains but this is obviously the worst case for this. At one point I had the spindle feed looped up with the dust extraction hose to keep it separate but wasn't happy with it. This is why you want to screen all the cables and ground them to a single point at the control box/VFD end. Capacitors in parallel with the limit switch inputs to the breakout board are a great help as well. My understanding is that it's the high frequency, high amplitude noise from the stepper and spindle drives couling back into the limit switch inputs and possibly then into the controlling computer that are the main risk.

Kit