Chris,
One idea/suggestion:
Your roof is likely "drooping". Essenstially, there is no support for the front of the roof at the moment, as the windscreen is not installed, so when you close the doors, the roof likely drops down some from the compression of the seals. Would suggest making a wood prop to hold the roof at the correct position while your assessing this. Then you can determine what the actual misalignment it. I would suggest doing this by setting the windscreen in place and sizing the prop so there is just still a small gap at the top of the screen. I kept my prop in for ALL fitment steps.
My two cents....
