Rick is correct. The input shaft will be the source of the whine in about 89% of all cases of this low RPM tranny whine. The noise that a throwout bearing would make is a high shrill squeal, similar to running your fingernails down a chalkboard. I would not worry about the noise. If you did not properly prepare the tranny cover/ boot when installing the shifter, you will experience more of the tranny noise escaping up and into the cabin of the car. Thus the increase in the numbers of Tranny Whines by people whom have recently installed shifters.
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1994 GT, Performance "Ticket" Red. Stock block with E-303 Cam, 351 "Boss Spec" Heads, Crane 1.7 Rockers, Cobra R Intake, Griffin Aluminum Radiator, BBK 70mm TB, FMS Aluminum Drive Shaft, FMS Clutch "Cobra", BBK Headers, BBK H-pipe, Pro 5.0 Shifter, Zoom Clutch Qradrant. All mating surfaces are port matched and clean, Car is lowered and is factory look. Sound sytem: Sony MD Head Unit, Sony 10-disc with memo Changer, Alpine DSP Equalizer and BBE Center, Image Dynamics Component Drivers (2high
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