Did you actually take the clutch basket out and the clutch plates? If not, that's where I'd start. Just a visual inspection under the cover with it all in place is not going to reveal the full story.

If the gearbox won't disengage from the engine's drive then it can only be the clutch mechanism. It is not going to be the gearbox at fault. If the gearbox was broken, jammed up or stuck, then you would still be able to disengage it from the engine using the clutch.

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