whine...........

Does in stop when you just barley apply pressure to the pedal or do you have to press it all the way in to stop it? Light pressure=throw out bearing, full pressure=clutch, sometimes the throwout and or new clutch will make a slight noise when they are new but usually goes away after a few miles. I have had this happen to me twice in my last 5.0 but it went away both times after a couple of hundred miles and no problems even on the 500+ hp motor.

When the clutch is in the tranny is disengaged from the flywheel. If it was the throwout bearing it would change tones when you just touch the pedal. Did they install a new clutch when you changed trannies? If they did, did they resurface your flywheel? If not this could be the problem if they did it sounds like something in the transmission. Just shots in the dark without actually hearing the noise.