I believe both cowls have already been replaced. Upper door alignment looks good, lower alignment looks good. Huge offset in the middle. Door in the middle sticks out about 1/2". Not. Sure what to do....

 

If the cowl piece has been replaced with aftermarket and the profile is NG it will have to be sliced and bowed out to match the door (as long as you know the door is correct).
I would fit the fender first as well to check the fitment there before cutting.

 

I'm not 100% sure just what I'm looking at. Are those photos of the same door showing the same non-alignment problem? Obviously, the first photo is at the driver side cowl. Is the second photo the driver side rear? Did you replace the latch-side door sheet metal at the driver door? If you didn't do anything to the latch side door opening, then maybe the problem is with the door.

 

Bodyman's way of checking: Take a long straightedge (metal yardstick or similar, make sure it is straight) place on edge vertically against doorskin behind post. Hold strong light at shallow angle to panel in front of and/or behind straight edge. Slowly rock the straightedge (SE) over the skin, watching the space between the skin and SE. If the skin is in good shape, the SE should rock smoothly and the spaces progress evenly. If the SE sort of bumps over it and/or the spaces suddenly change unequally, the skin has been distorted. Check the skin more about every 4-6" front to rear of the door. The curve should be similar at each station.
Quick way is to feel the surface with your hand. Place the entire palm and fingers of the hand flat on the panel, not just the fingers or finger tips, and slide around. To increase sensitivity lay a thin rag like a shop towel between palm and panel. The hand is very sensitive to even small variations when done this way. If skin is smooth and true, check cowl same way. If door skin has been damaged reworked, correct that before matching cowl. I suspect the door skin has been repaired at some time.

 

Pictures are of same area. Different angle. Door has not been replaced with any patch panels. Only cowls have been replaced. The rear gap door jam looks perfect also by the way.

 

Well, if the doors aren't the problem, then you'll need to rework the reworked cowl panels to match the door.