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As in you're adjusting where the how the window fits to the upper weatherstrip when it's up? You have to loosen the bolts that hold the glass to the regulator and slide the glass around- just trial and error to get it to fit right.
Three bolts. Two bolts on the bracket at the rear of the window glass and one in a recessed hole to hold the front glass stop bracket.
The way to adjust it is loosten all three bolts, then with the door shut, roll up the window until the gasket stops it. Do not go too tight ( where the back edge of the top starts to raise up ) or the back of the glass will kick out and make a gap.