I am also having problems with the windows fitting the car. I LOVE the hardtop but the windows have been a nightmare to fit to the car. My car is in Portland till Spring so I cannot continue to work on getting the windows to fit, but Steve @ Autoform has been very helpful when I call for assistance.
My drive down to Portland was in the rain and I felt it would have been better to have the top off than have it funnel in like it did. I plan on adding some additional seals and make more adjustments come spring time. My drivers door seems to be different than most and has been very troublesome to fit. The passenger door window was very close to fitting properly and hopefully the leaks will be found and plugged.
Call Steve and make him aware of your situation. Everyone at Autoform has been excellent to deal with and I am sure he will take care of you.
Mark