Whining Sound In Bellhousing Area

I have a supercharger type whining sound coming from the bellhousing area. Transmission has new main shaft bearings in it both front and rear and I also have a new throwout bearing. But this noise also was going on before I had the Trans Main shaft bearings and throwout bearing replaced. The noise does stop though when the clutch is pressed in. Anyone have a clue what would be causing this whining sound?

I thought about a new clutch when I had Trans out but never even looked at it because it was still working and grabbing great. Originally thought the whine was coming from a bad main shaft bearing because my trans had been ran low on fluid. Anyway it's a Ford Racing King Cobra installed in 2005 and probably has 20,000 miles or less on it.