I discovered - - thanks to a couple of very good mechanics at a VW Dealer was ... the window module is connected to the window motor. The problem I had was similar to your issues. One of the Techs said they would put in a Pw motor but once they put it in, I would own the motor. I went to my local Pull a Part yard and by luck they had a 2004 2.0L beetle convertible. I put it into my car, and knock on wood .. we have driven the car approx 3K miles and everything works great.
Good Luck
Wifes car is 2005 1.8L convertible, i
Good Luck
Wifes car is 2005 1.8L convertible, i