DriveSlow wrote:how exactly did you align the window? by just raising it up and down continuously or is there a part inside the window that you have to adjust?
There are three bolts that attach the window assembly to the frame. (two at the top, one at the bottom) These can be moved up and down, and the offset of the assembly against the frame can be offset by adjusting these odd bolts. This gives you 3 levels of control for each bolt. The bottom bolt, for example can draw the unit in or push it away from the frame, effectively pivoting the unit on the top two bolts and adjusting the tilt of the glass.
I've tried 3 times to align, and still need a slight adjustment. There are 3 things you are trying to accomplish: 1. Raised (up completely against the stops), the window should seat nicely against the door window glass. 2. Raised, the door should be able to open without contacting the rear window glass, and 3. With the roof up and secured, the glass needs to be far enough forward to rise up in the channel of the roof without getting stuck. There is NOT a lot of wiggle room here.
I would start by trying to get the quarter window aligned with the door window (top down, both windows raised.) make sure door opens without contacting the window. Then raise the roof and try to get the window to come up in the groove without getting stuck against the roof. Give yourself a lot of time for this. Every adjustment you make will effect the others. This may take hours to get right.