Dean one thing to pay attention to with mating different bottoms with uppers (in addition to the height issue your aware of) is that at some point between early ‘63 and early ‘65 (my two reference points) the bolt holes that hold the top section to the bottom section for the vertical members (4 bolts each) moved from directly
inline with the member (early ‘63) to
offset with the member (early ‘65). Not a big deal but you’d have to either fill and drill new holes if going from inline to offset or cut and move the mounting boss with holes on the top if going from offset to inline.
Pics probably help:
Early ‘63 - driver‘s side, note the position of the 4 bolts on the right vertical member
View attachment 2718451
Early ‘65 - driver’s side, note the position of the 4 bolts on the right vertical member
View attachment 2718453
They aren’t the same. Not sure what setup
late ‘63 doors have, but there are other differences like door handles as you know.