1989 Convertible Window Alignment

[89redmustang]

hi I am new to the forum but I am running into a bit of a problem with my main windows on my 1989 mustang convertible now after putting on some new weather striping this weekend. the problem that I am having is that when i go to roll the windows up the window wants to come in behind the weather strip on the pillar posts not on top of it and if i open the door and roll the windows up and then close them it seems like it is pinching the weather strip to tight. i have been messing around with the door and the track and nothing seems to be working to well. has anyone else had this issue or know how to angle the window so it doesn't pinch the weather strip to tightly.