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I had a similar problem. Check the track to make sure there isn't anything in there that is blocking it(a computer aerasol spray works great) and spray some type of lubricant to help a little.I found a little piece of a twig and it made the thing sqeek like hell and stopped it form going all the way back. Also did you completely unhook the motor or just unscrew it. What happened when mine did that it kept going back and forth. I'm sure you've read the other thread about how to fix it so you know that the computer has to reprogram the resolutions and get everything synchronized. So try unhooking the batter then hooking the motor back in screws and all after you have sprayed out the tracks and lubricated them then see how that works.
Also when you put the motor back in the motor is at the right position that the roof is in.(i.e. if the sunroof is all the way back then the motor is in the fully open position)
Hope that helps.
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