I'm trying to align the driver's side quarter, door, and vent windows on my 67 convertible. The vent window is as far forward as it should be, yet the door window is still too far back. The door won't close because the door window hits the quarter window. I followed the alignment instructions in the Service Manual, but no luck. Any ideas?

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Looking at your photo, you first need to align the door. Its way off and this can be due to bad bushings in the hinges or just not adjusted right. To check the bushings, with the door open, lift up on it and see if you have any play, if so, they are worn out. Replace them and re-adjust the door to where it should be. The striker may be off also and require some attention. Once you do this, you will see a change in the window alignment also.