The late 3.9's in a D1 have all the bits including bosses for the knock sensors, but the crank pickup housing needs changing if you are going to fit Thor Bosch ECU etc.
D2 housing is EIQ100020 and I have one on my desk. The PCD of the flywheel pickup drillings is different on a D2 flywheel.
The pickup housing is the only difference I found when I fitted a late D1 short engine to my D2.
Peter