Why do these companies using ECUs in their diggers not isolate the ECU from the chassis using rubber fixing points then earth through the standard connectors. Then all the operator would have to do is disconnect the electrical connectors to ECU and it would be totally isolated from any electrical interference?
As for the post, have you tried testing the stepper motor? You don't need the ECU to drive it you can simply measure resistance on each of the coils, or apply a voltage to move the stepper motor. If measuring the resistance of each of the coils they should be about the same, if not then this could indicate potential problems. Not an easy thing to test, but do-able all the same, but make sure you understand which pins you need to be testing. Without looking I cannot advise as I'm not familiar with these machines.
Hopefully you manage to sort the problem and have the machine back up and running. Sorry if I went a little of track.