I PUT A 2000 5 SERIES BMW MOTOR IN MY 3 SERIES 1999 BMW AND USED THE WIRING HARNESS OFF THE ORIGINAL 3 SERIES WHICH I HAD TO AND NOW THE STARTS AND IDLES FINE WHEN YOU REV IT UP IT SPITS AND SPUTTERS

Did you do the swap? Did a mechanic? The software may be the biggest difference here. Were they both automatics? Again, software can be the biggest culprit of engine performance or lack of performance. Either way, get it to a shop ASAP.

What motor did you swap over? Really need more information in order to help you out. Many things could be causing this issue, Fuel pressure, mass airflow sensor, ignition system and timing. This can get complicated in a hurry also give us the fault code numbers and a better description on what they are.

The engines of a 3 or 5 series are the same. They may vary on the accessories and intake or some sensors. In you can check the original engine's intake for differences do it. Also check for leakage in the intake which causes engine sputter and detonations.check the fuel pressure to be sure and also Check the mil codes for more help