If anybody else had a feeling that the doors didn't look quite right in the previous pictures I was having the same thoughts! In the end after repainting and then re-clearing they have come out right. I also wet-sanded and machine polished the whole car so I can start refitting brightwork and other fittings...
Much better!
Door windows in, it was like doing a 3D jigsaw puzzle that would only go together in a particular sequence!
I've put in all the door hinge screw not too and am really please with how the doors line up with the rear quarter panels, the swage line is perfect. I just need to pack up the rear body spacer a small amount to get the door gap parallel.