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try a spray lubricant into the motor mechanism and grease any visable wire cables that run from/to motor ,not the electrical cables the bare wire winder cables,also grease/ lubricate any accessable pivot/hinge points , gently pull the cord and gently push the roof back and forth occasionally trying motor with a bit of patience this should get the roof moving , also look for anything that may be snagging the roof/mechanism as there is a pressure protection system to stop the roof being fully closed on say someones hand so preventing injury
there is a microswitch on the right side under roof cover if roof cover not fully down boot is locked shut by microswitch you might be able to press on cover and you may here boot lock solinoid click off get some one to push boot lock if you can.t reach when you get in boot /trunk you should see small wire that travels across rear bulkhead disconnect this and trunk/boot lid will open but roof will not obviasly i,ve worked on one of these all day today and have had every thing wrong with roof you could imagine good luck
No doubt your soft top issue has long been resolved but just in case someone has a similar issue:
I started to open my A4 Soft top externally using the door key method and like an idiot I must have disengaged the key before the soft top was fully down. I was unable to activate the opening or closing of the soft top automatically using either the key or soft top switch inside. I then manually closed the soft top using the users handbook and manual tool supplied. Soft top would still Not open automatically and the soft top alarm would activate. I solved the issue by manually opening the soft top fully and then manually closing the soft top fully. This seemed to have reset whatever had gone askew.
It is never a good idea to unplug your modules with the key on you definitely can damage them. Hope fully your windows are not synchronized. See if the express mode up works. Try holding the button in the first detent and raise window and hold for 5 seconds. next see if the windows work with the 1 touch operation. It is possible that the module you unplugged stores the synch for that feature. The soft top module must know the window position in order to operate. Also there is a sliding cover that must be retracted in your trunk in order to operate top. The switch in the cover has to be depressed to let module know that there is nothing in they way of the top operation. Hopefully I have been helpful.
If you hear the motor then you can almost certainly rule out electrical issues, it souonds more likely that the roof panel or drive mechanism is jammed or stuck, If the roof is closed then push up on the rear of the sunroof and see if it "pops up" a bit then while still pushing up hit the button to open.If it is anywhere in between open and closed try pushing it open or pulling it closed while you are pushing the button,if it moves inspect the tracks and lubricate