Haha, finally figured it out. After swapping a couple of parts and trying to figure out which microswitch was the problem, I bought one of the cheap vag-com cables and was able to see that the switches were giving the right signals. I took the front locking assembly apart and found that the motor was seized. I was able to get some WD40 in it and hit it with a jumper wire to work it back and forth and once I got it reinstalled has been working fine. Even cleared the error codes so that it stops beeping every time we start moving. Now it's time to put the new top on. Haven't decided if I am going to tackle this myself or get quotes from some local top shops.

 

Wow.. Good stuff fellas. I am starting to have the same issue with my 2008 Audi A4 Cabriolet. It will release from the windshield but quit going half way through. I will try the pump firs.t Hope this does it.
I will get the vin and put it on here.

 

Hello! My roof would unlatch but was not opening properly even after manual reset. Dealership and Audi specialist recommended changing pump and motor. I did buy a rebuilt pump and motor for a fraction of the price. Installed it and bled the system. The roof opens but now, the problem is that the rear roof cover, once opened, closes before the rear window and roof are fully retracted. Full opening cycle cannot be completed. My guess is that the potentiometer (position switch) is faulty. I checked the resistance across the potentiometer (position switch) and the resistance reading changes while opening or closing the angle of switch but without having the original specs of the switch, hard to figure out if the signal is correct. Should I assume that the position switch is faulty and buy a new one??
Thanks!!