Yes the shaft turns at flywheel speed but if the pilot bearing is breaking up and not centralising it there is a possibility that it will be out of line and be putting pressure on the front gearbox bearing. This is why I asked if changed, maybe unpredictably, when you declutch. Do you get any odd noises when you reverse it up a steepish slope, up into a driveway perhaps, when slipping the clutch. Humour me here but that can also be signs of a bad pilot bearing.
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