Dennis,
I am facing an almost identical problem as you on my 29 Tudor. I too have replaced full length subrails, rear cross channel, cowls, and the lower 6" of all body panels. That means I am aligning everything from scratch.
I notice your body may be temp mounted on wooden blocks/frame? I would suggest not bending anything until it is mounted on the chassis so you can align the doors when they are in their 'final' position.
My probelm door has been cracked around the check strap mount so the front edge hinge 'face' isn't square any more. I will repair this first. Also, is your A pillar bolted in its final position? If it is slightly twisted it will affect the hinge alignment.
If you need to 'open' the lower hinge to allow room, consider that the door will be slightly lifted at the back edge. A rag in the hinge when you close the door can do the job nicely so I am told.
Good luck.
Gus