The two different types of engines are The SBEC controller type, and the NGC controller type. The differences beween the two engines are the crankshaft position sensor tone wheel/flex plate/ ring gear. and the cam shafty position sensor sprocket. The tone wheel that connects at the crankshaft may be wrong.
The other concerns that may cause this concern could be restricted catalytic converters,. Low fuel pressure , possible timing not in spec.
Have you had the computer scanned? Whats the fuel pressure,?
The Crankshafts are the same. I recommend taking the car to a large dodge dealer and ask them to diagnose the problem. It could take an hour or two of labor -And the problem is diagnosed . Make sure you tell them about the engine swap and you want the cam and crank sensors scoped and the patterns checked. The pattern is located at the end of the diagnostic manual . Please Click accept, Thanks Scott.