Drive Pinion Stem and Pinion Flange
WARNING: This page is about a different car, the 2006 Ford Pickup, 2006 Ford F550 Super Duty, 2006 Ford F450 Super Duty, and 2006 Ford Cab & Chassis. However, it is still accessible from the selected car via links, so may be relevant.
Check the pinion flange runout when all other checks have failed to show the cause of vibration.