Once the lower door is aligned front & back, check the upper frame's contact with the door seal. If necessary, bend the frame gently to acheive even contact with the door seal.
That's my footprint near the sill button hole. I couldn't get a picture of me sitting in the seat with a foot on the door & a hand on the frame, and you probably wouldn't want to see that anyway. :-)
For door alignment, see this post:
http://www.fourdoorbronco.com/board/showthread.php?6884-Door-AlignmentFor more pics of this door being installed & aligned, see this album:
http://www.supermotors.net/registry/2742/66137-4Door Panel Removal

This is the last pic that deals with door alignment.