Upon converting an '82 240D (Manual) to an upgraded 300D-T, we have most of the bugs worked out. She fires instantly and runs out nicely. However, we have one issue that we can't figure out.
At idle and upon take off, there is a rather major vibration. It almost reminds me of one of my other MB's that had a driver's side engine mount missing. The car would vibrate the heck out of you until the rpm's were sufficient to lift the engine off the frame.

1. I did not balance the flywheel because I couldn't find any marks. However, wouldn't this affect vibration at all rpm's? After 1500 rpm's, the car runs out smoothly.
The harmonics of the motor mounts and the mass of the engine may be such that the vibration is masked at higher RPMs. IMHO, you need to pull that tranny and flywheel, find those marks and reassemble. See this thread for a pic of the flywheel mark; it was hard to spot on this particular flywheel becasue it was obscured by a lot of clutch dust: http://www.peachparts.com/shopforum/showthread.php?s=&threadid=77924

2. I have new motor mounts
Great, at least you know it isn't the mounts!

3. I had to fabricate/adjust the former crossmember holding the tranny mount. I drilled holes 1" narrower. In the end, this mount might be 1/2 to 1" higher (closer to the bottom of the car) than it was.
Not the source of your vibration unless the transmission is actually touching the body somewhere. But, this sounds like you'll eventually have a driveline problem. The flex disks aren't intended to function as a universal and any misalignment through the disk will result in driveline vibration and premature failure of the disk. Raising the back of the transmission that much will cause a misalignment issue.

__________________
Never a dull moment at Berry Hill Farm.