I just have to believe that the transmission needs to be pared up with the engine that it was designed to work with. I think it's the same issue that you have now with the 3.0 engine working properly with a tranmssion that was used with a different engine.
Just know that I'm not a technician. I stayed at a Holiday Inn Express last night.
2001 E430, Bourdeaux Red, Oyster interior.
1973 280SE 4.5, 170,000 miles. 568 Signal Red, Black MB Tex. "The Red Baron".