The possibility that this sort of interference would mess up the function of the low level board has me thinking of separate boxes for the low level and high level parts of the device.
Lossy ferrite cores threaded over leads are popular at low power levels for surpressing hash. For this, we need a 1 inch hole to allow clearance on 4-0 insulated welding cable, and the toroids used for transformer cores will not do. I'll try to search out some large RFI lossy toroids. This outfit has some with .90 ID, but the permeability can be from 40 to 10,000. For this RFI surpression application, I'm not sure what to try.
Ferrite Toroidal Cores : CWS ByteMark, largest supplier of toroids, ferrite cores, iron powder cores, MPP cores and RF cores
Slipping one or more of these on each power lead of the controller should help the external RFI issue, subject to fines from the FCC if not kept appropriately down.
bob