You don't need any scan tool for this. (There is no connection between the smart motor and the diagnostic bus.)
The window initialization allows the smart motor to learn the normal and stall currents. This is so it can detect when someone or something is caught in the window. You accomplish it by holding the button down for several seconds and up for several seconds, at worst.
There is also motor indexing. This gets the smart motor correctly set to know where fully and fully down are. This was likely your problem the begin with, based on your symptoms. Basically, roll the glass all the way up, disengage the motor mechanically from the regulator, press auto up and wait for the motor to stop, then reinstall the motor.
What ever you have going on now is something else. Either the regulator is mechanically hosed, the smart motor is dead, or there's a problem in the wiring or switches. It's easy to mess up the regulator when you take the motor off if you aren't used to how it has to be handled to keep the cable from unspooling or cross winding on the reel.