Same issues as most with the window motors, mine were going up and down, but then back down by self - replaced with non-standard motors and have been good for 3 years now.
Throttle body was completely cracked replaced by non VW shop and all is good.
Original radio was junk - would say no CD/tape in use when CD/tape was in use. replaced with Sony and all is good.
Biggest issue is the door trim that is stuck on with cheap tape.
I love my car and haven't really had "major" issues out of it. still gets great MPG even with 89000 miles on it.
Where did you get the non OEM window motors from?