All you're saying points to the transmission. If you don't have the clutch pressed in, the revs of the engine continue to the tranny. When you have the clutch pressed in, the tranny and engine are not connected. The fact the noise stops when you have the clutch pressed in, makes me think the tranny is your issue.
How many miles?
How's the tranny lube?
Have you checked the level or changed it?
I had a Dodge Raider that whined in every gear. It sounded like an old dump truck! It went that way for a looong time until it wouldn't go into 4th so I changed the tranny. The whining then stopped.
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