Dave,
You must either have too many shims between the body and the frame at the A pillar, no shims or the incorrect thickness of shims at the B pillar and at all body to frame mounting points towards the rear of the car from the B pillar back, or a bent up frame somewhere in the back half of the car. I would think that by removing the mounting bolts from the B pillar back and reshimming each side of the car separately until you get a good door gap at the top rear of each door should resolve your problem, provided that there hasn't been any frame damage. All body off restorations of small birds in our shop are reassembled with new body rubber/shims that are all of the same thickness, and we've never had the problem you discuss. Question: do you have a continental kit installed on the car, and its extra weight has bent the frame up in the middle of the car?
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