I had weird high pitched vibrations coming from my shifter, the higher the RPM on the highway, the more it whined. It sounded like a jet plane.
I had defective halfshafts and wheelhubs, ford replaced both and the vibe and whine went away. Take it for what it's worth.... not saying that was the fix, maybe something wasn't torqued right in the rear and the vibration travelled to the shifter. This was when the car was stock except for a K&N filter back in 2003.