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Try readjusting it. They lines don't alway line up perfectly. It could be other things too. Was the moulding installed correctly on the front pillar? Is the birdcage rotted or has it been replaced? The door gap at the back seems tight. 1/8 tilt towards the front will be barely noticable on the rear. It takes a lot of playing with to get it right.
You need to follow the adjustment proceedure to the letter. Its posted in these forums somewhere.
This is the only link I can find. There is a better and easier one to follow but I can't find it.
Did you try adjusting this bolt and the one next to it?
I can tell by the position of the circled bolt that you have the angle down to far in the front. Loosen off both those bolts....not just the one....there is another one to the left out of the picture. Take off the T top and pull the window up into place. These two bolts control the tilt of the glass. You will notice it rocks back and forth. If you can not get the glass pulled up, loosen off the stop on the front track as well. Pull the window up into place, then enter through the passengerside and tighten those two bolts and the stop. See if that helps. Once done put the T top back on and make sure the front clamp of the T top is is adjusted right to pull the T top down snug....do you have the rubber on the end of the T top stop bolt? You still won't be done though....you still need some minor adjustments to the in/out.