Moving _once_ when power is plugged in, but not buzzing, does not suggest a problem, with this version of the controller board.
Can you please clarify why it is that you cannot get past the warning? It’s a warning message, not an error, and does not prevent anything else from working. If it’s just bothering you so much that you cannot get past it, then let’s temporarily disable that warning, so that you can move along. Otherwise, just ignore it for the moment.
You are correct that there are no directions in the user guide for connecting or replacing the pen-lift motor.
The “first two steps” are connecting the cable and installing the pen clip. That is why the directions there are for how to connect the cable and install the pen clip.