First make sure that you don't have any kinks in the channels.
Next loosen all of the screws which hold the window regulator in place, and roll the window up. This will self-align the glass in the window opening.
Tighten the screws.
BTW, how did you secure the channels to the window opening? I use short self tapping screws and use an electric drill with a screwdriver bit.
Carl


1952 5-window - return to "as built" condition | 1950 3100 with a 235 and a T-5 transmission