Some reproduction door shells don't fit like originals and hence have problems (door catches on front fender at the belt line, etc.) A good body shop can make these useable but they won't look as good as an original door.
Window weatherstrip can leave gaps if the window isn't adjusted correctly or has a repro weatherstrip tip at the top edge of the vent window frame. Possible corrective action: adjust the window stops inside the doors for correct window height at both front and back of the window. This will work if the vent window frame has not been removed (in most cases). If the vent window frame has been removed or replaced then it may require adjustment to a taller height before the main glass height is adjusted. If the weatherstrip tip halts window movement, take it off then adjust upper stops. In the extreme, you'll have to shim the roofline channel and install the weatherstrip fractionally lower than before in addition to making adjustments. Now if the roof has been changed, you may never achieve a satisfactory seal.