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When I roll up both driver and passenger windows on my 67 roadster the window glass begins to rub on the softtop weatherstrips. This happens about one inch from the end of the window run. I believe the soft top is out of alignment. Is there such a thing and is it correctable without major surgery??
The top can be adjusted at the rear lock pillars on each side. However messing with these could compromise the way your top fits. (Cause wrinkles in the vinyl or plastic window) The best time to adjust the top is when the vinyl is off and the windows are both up. Obviously done before a vinyl top change. I'm not quite sure what your problem is but your windows can be easily adjusted (back and front and in and out). It's been a while since I had my door panels off but if you remove yours you can see how they are adjusted. I would consider adjusting the windows before adjusting the top if this will solve your problem. Good luck and let us know if this solved the problem.
I just got my door panels put back on after messing with the windows. I'm here to tell ya....there's about a dozen ways to adjust these windows and all have pros and cons....you pull it in a little here and it sticks out over there. Snug up this bolt and that bolt binds....It took me several tries, SEVERAL BEERS, and finally a wife who said "who cares, you never have the top up anyway...."
I finally found a good compromise in all the adjustments. However, what finally helped is when I do roll the window up I first loosen the top latch on the soft top. Once the window is fully up I tighten the latch and the top has not choice but to snug up to the window.
The other adjustment, as mentioned above, should be the whole top frame prior to installing the soft top itself.