I have the MTU connected to the Bodnar Cards and last step is connecting the Stepper Motors to the Arduino and then MobiFlight. I have never used Arduino or MobiFlight. I've searched the Forum and reviewed the info on Throttle5 Build Guide.
1) Do I need MobiFlight if I have Prosim?
2) Would you mind sharing your Arduino Sketch so I can see how you've setup the Stepper Motors?