For every action there is a reaction. Are you mounting a hard top or no top? Windshield to door gap is a function of angle of windshield frame and position of door. If you have a hard top, you can set the angle by where the frame mounts to the top (and slightly modify the mounting position). If you are running topless, you need support arms coming from your roll bar (which should also be adjustable (Hiem Joints).. Either way, I don't think you will have an issue. Pics would tell us more, but you may find that once you get hood, grill, fenders, and doors aligned, windshield frame is fine. Key is that your door drives the windshield gap (as you note) and then the angle the windshield gap is whatever is required to make the gap parallel to the door frame. On mine, the windshield gap on the DS was a perfect 5/16" all the way up, but the PS actually touched the door frame. I got into the Bronco and "twisted the windshield frame by hand, pulling on the drivers side while pushing out on the passenger side. I also had my windshield frame off and reattached it with multiple low profile self tapping screws. So one can make some minor adjustment on how the frame is mounted to the cowl, but very minor.
Here are mine, and as I said, they started out way off.
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