So the top of the door is fitting flush, but just the bottom rear corner is protruding? A photo would sure help. We really have to see it to make an accurate diagnosis.
Was the door damaged at some time in its life? Or did it come off a different vehicle? Is the door actually the problem, or is it really in the body itself? Do you have another door you could try to see if it fits the same? This would identify whether the door is high or the body is low.
If only one corner is protruding, the worst-case scenario is that you'd have to reconfigure the door by pie-cutting the inner panel, bending the door to shape, then re-welding.
