As painful as it may be sometimes rework from square one is the best overall option. Most, if not all of us here have been in the same spot with one or another tasks on these metal chunks at one time or another. From my learning experience in reassembling my ‘46, one step leads to the next and they all have to fit properly or the ripple effect for problems just grows. My guess in this case door alignment problems will at some point lead to door latch problems, which will lead to locking problems, along the way rocker panel fit might add to the adventure and then will come fender, hood and grill alignment challenges. Good luck and keep us posted.