Regarding bearings... they said when the planned repair was complete, the car failed the mechanic's test drive because of an additional bearing that needed to replaced. Took an extra week to get the car back because of that.Sounds like something's wrong inside the transmission to me. It shouldn't be making a whining noise. Did they replace the bearings in the transmission?
The hum when the engine is running and transmission is in neutral with the clutch out also sounds like a transmission bearing issue to me. Another possibility is they didn't shim something properly and one of the shafts isn't preloaded as it should be.
Parts list below, there are a few bearing assemblies...