Thanks Kevin, the pinion gear is part of a repair kit that I installed and I installed new plastic rollers that engage the tracks so I suspect that I have "fixed" myself into a problem without an easy solution.
I agree that it is probably something caught int he pinion gear but it is impossible to see given the lack of access.
I have tried unbolting the window crank area but it can not move much due to the formed pocket in the door steel that it sits in. I do not beleive I unbolted both at the same time so I may try that. I also may try fishing a magnet into the pinion area to see if I can relocate what ever is caught in that area.