Did you have any clutch/transmission work done recently?
Sounds like your pilot bearing. It mates the crankshaft to the input shaft of the transmission and only spins when the clutch is pressed in (allowing crank and input shaft to spin at different speeds).
Check here for tips on removing the old bearing (it can be a pain in the rear):
http://forums.mustangworks.com/showt...ighlight=pilot
Good luck,
Rich D.