After checking the previously suggested problem areas ask yourself a couple questons.
First: Did you have the machine shop balance the rotating assembly when the engine was rebuilt? If not, and major components like pistons were replaced, that could be the cause of the problem.
Second: If the vibration is not engine related and only occurs at a particular speed, make sure you didn't over torque the drive shaft bolts. The U-bolts holding the driveshaft to the pinion yoke only require 17 foot pounds of torque and no more. Over tightening these bolts can easily cause a drive train vibration. Been there, done that.