Common e30 drive shaft vibration. I assume you had to separate the front and rear as the swap requires a new front section, so did you align the u-joints correctly?. From factory they were supposedly balanced separately so others will disagree with me saying they have to be aligned. If you look in the Bentley there is a diagram on how to align the u-joint knuckles when you separate the two sides. Also, did you preload the CSB when you installed the driveshaft?
While you have the drive shaft apart again manually oscillate the u-joints and feel for notchy-ness. A sticky u-joint can cause quite the rucknus! In your case the sticking may be very slight.
The drive shaft could just be bitched as it's probably 25 years old...