If you pop of the A pillar there are two clips and a torques 25 that holds it down. My guess is one of those clips is not snapped in, most likely the clip is broken causing it to just bow out. As far as the roof, is it along the side or the center? If its coming from either side you can remove the handles from the roof which will either be a torques or a Philips head and just pull downward on the door seal and you will be able to inspect up there. I had one customer who had a rattling right above his head and when I removed the handle and inspected it I found a piece of plastic that was supposed to be glued to the head liner as a support fixture was no longer attached causing a wicked rattling noise.
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