I'm curious that the bearing's make noise when not engaged. The Clutch Release Bearing (throwout) shouldn't be making contact and therefore just sitting on the front shaft housing (Main Drive Gear Bearing Retainer). When you press the pedal, the bearing contacts the clutch Release Levers and begins to spin. It spins at engine speed as long as you keep the pedal pressed. Then it stops spinning when you let the pedal out and the bearing is no longer in contact with the clutch.
Do you have the clutch pedal adjusted to have 1.5" free pedal before you feel the resistance from making contact?
When you separated the transmission and engine, did you replace the pilot bushing also? Odly enough, the pilot bushing would be exact opposite of the throwout bearing; quiet when driving but possibly noisy when clutch is engaged allowing the flywheel to spin on a stationary Main Drive.
I do believe if you open the sealed throwout bearing, it will eventually fail.
As I've not been on for a while, I'm curious if you're still working this or did you resolve it?