Dince the facotry never built a 440 Duster you have a combination of drive train parts that likely weren't married at the factory. One thing that could be causing your shifting problems is if the bell housing was not registered to the center line of the crank. Mopar used offset bushings to move the bell housing around so it was centered. If the bell housing is off then the input shaft of the tranny could be dragging on the pilot bushing not allowing the input shaft to stop turning between shifts.
If you wind up pulling the tranny check the registration before tearing into the tranny for a rebuild.