It sounds like your regulator is not aligned correctly and not riveted in all the needed places. It could also be that your door metal has a crack in it, and when the window raises to a certain level, the metal in the door can't support it and it gets out of alignment. I have done this type of work at a GM dealership and replacing and repairing these window is pretty tricky, so go back and really retrace all your steps. Did you follow the instructions in the service manual , when you did this, because there are instructions for how to adjust and align the window and the regulator.