Compass/Motor Calibration Failed: Initiating Ardupilot

Using a MATEKSYS H7A3-SLIM flight controller and a Mateksys GNSS M9N-5883 compass. Using Ardupilot MP to configure flight controller.

Currently, the compass onboard the quadcopter is experiencing a lot of EMF noise coming from the battery connection and the three phase wire to the motors. Unfortunately, space is a huge constraint in this case, so it is not feasible to move the wires physically away from the EMI sources. The issues arises when I use the Compass/Motor Calibration tool within the Setup → Optional Hardware section on MP. I followed the instructions listed here:

However, whenever I follow those instructions, the dialogue prompt constantly displays the text “Initiating Ardupilot” every time it auto-refreshes. It is never able to fully initialize the Ardupilot and always end up in me ending the procedure. I am doing this through a wired connection.

Is there something that I am doing wrong here? Any and all help is welcomed!

Page all the way down in that link to Magfit and use that.