Did you change the motor mounts?
Put a block of wood on the oil pan and then jack up a little with floor jack and see if vibration changes.
BTW, once upon a time I had to retighten the motor mounts on my Sportster....... Afterwards the speed at which the mirrors vibrated the most changed....
So, you may have changed the natural frequency of your bolted in engine............
If the vibration changed with the floor jack, you may be able to change the vibration by loosening and redoing the motor mounts when some of the load is supported by floor jack.
