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Remove the transmission, clean the pilot bearing/bushing, input shaft, front bearing retainer tube, fork, pivot, grease said parts, reinstall as you removed those parts.
I recommend replacing the pilot bushing, clutch disc, and pressure plate while you're in there if they have appreciable or unknown miles on them. At minimum inspect and clean them and inspect the flywheel for wear, warping, or hot spots. Also check the input shaft for play. Wiggle it around side to side, if it moves the mainshaft and pocket bearings in the trans are worn out, and probably all the others as well.
Are you sure it is the throw out bearing?
1. Noise stops when the clutch pedal is depressed could be transmission bearings.
2. Noise begins or gets worse when clutch is depressed, most likely related to throw out bearing or pressure plate.
You can check whether it is the throwout bearing by removing the clutch slave cylinder (or disconnecting the mechanical linkage for earlier trucks) and moving the throwout bearing away from the pressure plate by pulling the outward end of the fork towards the front of the vehicle. You can look through the fork hole in the bellhousing or the inspection plate to verify no contact between throwout bearing and pressure plate. Then fire it up, being sure it's in neutral and not touching the clutch pedal, and see if the noise persists. If it does, the noise is not the throwout bearing.
Thanks for adding that cadunkle. I have seen too many people change out the TOB (and clutch/PPwhile they are there) only to continue to hear the transmission bearing noise when they are finished.
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