I'd suspect the throw-out bearing. It spins all the time, but really loads up when you push the clutch pedal in. That'd make it squeal louder, I'll bet.
I've never had a bad one, so I can't tell you for sure. I'd hate to guess wrong on that one...that's a lot of tearing apart to diagnose. Might as well do a flywheel swap or clutch replacement while you're in there...