Glad to know mine isn't the only Mustang with an electrical gremlin. I would say it took a year and a half to take care of them, but I don't want to jinx it.

 

So the auto button not working is a separate problem from the window not moving up or down all the way. Ford released instructions on how to reprogram the window such that the window travel is relearned. This process is really a two person job. If someone has the link to it, it would probably be good to post here.

The problem I had was with the switch only where 1 of the 4 positions was only intermittently working. That position being the auto up button.