It could be the Flywheel out of balance. Some engines are sensitive to how the flywheel is installed. If,after checking other things and you still have the vibration, you might try unbolting the flywheel and rotate it 180 degrees. ( I am ASSuming that it does not have a dowel to locate it) If the flywheel is the culprit, that will either reduce the vibration or shift it to different RPM range.
Some other thougnts: Rebuilt engine with mismatched pistons (one heavier than other), pressure plate/clutch out of balance, vibration damper, crank balance
Good luck
