Before any work is started I place a strip of masking tap on the door and body, cut it at the seam. I do all that can be done with the body on the frame. If the tape still lines up nothing has shifted. Take the body off, finish the remaining work, finish the underside, get the frame finished, cover it with a large sheet of plastic, set the body on, assemble all the sheet metal, now start tightening the body mount bolts. The body mounts at the cowl will play a major roll in door alignment, the jamb area specifically. I like to start in the middle of the car and work back then forward. Getting the mounts even (torque) in the middle first gives a good starting point. The front and rear mounts do not necessarily carry the same torque. Watching the quarters and door jamb gaps will tell you which way to go with respect to torque on them. On sedans the alignment of the top of the door to the roof line is really affected by the cowl and hinge mounts and the mid body mounts. Adding or removing shims in the middle will impact that gap.
Bottom line, there is NO set rule for re-mounting the body and getting things to "fit" right. Just have to keep working on it until it all fits.