05-17-14: Thebambino
Fixed. In case anyone ever pulls apart the motor, it's really a simple beast. What happened was when I took off the brass nut that sits under the pulley, it allows the drive shaft to lower to the very bottom of the motor casing, creating a vibration. You have to manually hold up the drive shaft while you re-attach the set screw, and it holds the drive shaft a few mm above the bottom housing of the motor base.
So is the brass spacer under the pulley still off? I have the same clicking noise when the motor starts up with the new pulley. So you are saying I need to lift the motor shaft up and push the pulley down before tightening the pulley set screws? Should I take the brass spacer off? That sounds like a tricky operation, there's not much room in there.