Door Alignment Problem - 65 Dart Convertible

1st. thing to remember is that panel fit and production tolerances were horrible on a-bodies all the way into the 70s (all american cars actually).

2nd. Align the door to the 1/4 and the rocker then align the fender to the door.

Your replacement door could also have a twist in it (not uncommon given craptastic production tolerances)