If this was a manual 240d before you did the clutch job and I think it was. I believe the flywheels where neutrally balanced on some and not on others. Hard to get a clear picture on this.

My understanding is that there Is only a very faint reference mark on them for correct orientation. Obviously you pulled the flywheel for resurfacing. If you paid no attention to positioning when removing and remounting the flywheel there may be a balance issue here. Some members have claimed that mark is really so faint on 240ds it is hard to even find.

Always mark orientation with a punch or paint when pulling and installing flywheels if you do not locate a mark. Personally I have never done a flywheel removal and re installation on a 240d. Since you have issues with the clutch disengaged it is either the flywheel orientation or a real imbalance in the pressure plate creating the change. Not a great chance of a new pressure plate assembly being imbalanced.