At least with a Sportster you do not have to line up the upper half of the door with the windscreen- the top of my door was probably 10mm out, when the bottom/centre was flush.
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[url=http://www.flickr.com/photos/mikes_bmw_marlin_cabrio/5313949662/]
Nearside Door Prior To Reworking
I cut my door open, used a couple of wooden splints to pull it in to the shape I wanted:
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Nearside door cut to rework panel lines by
Mike's Marlin BMW Cabrio, on Flickr[/IMG]
And then re-welded it: Its not perfect, but it is much closer than it was before!, and the shut line are parallel in all three planes.
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Shut Lines by
Mike's Marlin BMW Cabrio, on Flickr[/IMG]