Next time you repair cowls do it with the body bolted to the frame and test fit the doors before you finish weld the parts. I screwed all my replacement panels on and test fitted the doors before I ever got near mine with a welder.
Since the hinge pillar determines the alignment of the rear edge of the door it doesn't have to be off very much to have a big effect. You could try shimming but if the door opening isn't right the door is going to require major edge work to get the gap right.
If you're 1/2" low in the back you're in for a lot of reworking.
