Each mount does indeed have mounting/locating pins/dowels, so just jack engine with a block of wood between sump/jack then simply loosen the nuts either end of the mount and rotate if need to align the pins, they are there to unsure people don't fit the mounts upside down, but if resting on a pin due to not being aligned it won't give this vibration, there is normally a gap between the arm and mount anyway.
Is the vibration in every gear ?, sounds more like the gearbox to me, good/new mounts will keep it to a minimum though.
tabetha