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I have some issues with my window alignment as well, I bookmarked the following article to use as a reference when I get a chance to work on it. Hope it helps out
Also, in case you are interested, if you do a search in this forum, you'll find a thread about converting the power windows over to crank, which is what I am going to try sometime in the hopefully not too distant future. Saves weight, less wires to worry about, and generally, no more worries about rolling your window down, only to find, one day, that they won't roll back up...
Posted this before doing a search. Search says that my rollers must be worn out. Just more $$$ and time.
Do you have the AIM for your car? There is a good procedure in it for adjusting the windows. If you don't have it, PM me your email address and I will email it to you.
I found the scans of the AIM. Go through the procedure 2 or 3 times to zero in on the "perfect" alignment.