Noise when you push the clutch in is sign of a bad pilot bearing. When the clutch is engaged (pedal up), the pilot and the input spin as one, when you disengage the clutch (push pedal to floor) the input spins at a different rate than the crank and that is what the pilot bearing is for. Your TOB would be making noise all the time if it was going out as a properly adjusted TOB is always spinning.
2000 Mustang GT Steeda #0048 34k miles. 99 Cobra 4V swapped, FTBR IRS swapped, exhaust, tuned by James Gordon.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.