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Installed all new wheather stripping all the way around the car (88 targa top) Problem is that now the windows are slow and won't go up 100% if door is closed, doors are hard to close and the rear hatch is hard to close.
Question is what is the best way to get these to break in and get things working again?
Carefully close evertything up and let it sit in a warm place for a couple of days. The new weatherstripping will "learn" how to interact with the other contacting parts over the course of time.
The same thing happend when I put new windshield weatherstripping on my vert. I could hardly get the soft top to close and thought that I might crack the windshield or pop the mounting points out of the window frame when I closed the locking levers. I really had to lean on the top to get it to close. Once I got it closed, I left it closed for a week. After that it was fine.
If the above suggestion doesn't work, you can adjust the hatch latch, and the angle of the side windows. I bet over time they have been adjusted to the old weatherstripping and now don't fit correctly due to the previous adjusting. The hatch is easy to adjust, just remove the rear trim piece and there are I believe ( it's been awhile since I adjusted mine) two bolts that secure the latch in the vertical position. Loosen these and adjust them up a small amount and try closing the hatch, repeat until acceptable. Take it for a spin after to make sure you don't get any wind leaks. The windows are more of a pain and I would see if the new weatherstrip takes a "set" before I dove into that one.