If the noise comes and goes with clutch pedal action it's most likely the throw out bearing. Pilot bearing would squeal all the time if it was bad
A pilot bushing would only squeal when the clutch is depressed. The rest of the time the input shaft is turning the same speed as the engine. Do the manuals have pilot bushings or pilot bearings? A pilot bushing will squeal, while a pilot bearing will grind - but you likely wouldn't hear it. The synchros would grind as you move the shifter into a specific gear. If it's grinding while the clutch pedal is down, it's likely the throwout bearing, but if it's bad enough a throwout can grind whenever the engine is running. A mainshaft bearing will grind while the vehicle's in motion with the clutch in or out. An input or countershaft bearing will grind with the clutch out, sitting in neutral, or rolling with the clutch depressed, but in gear while coasting.
It's been a few years since I've thought this stuff through, so feel free to tell me if I'm wrong.