Quoted from spblat:
My supercharger was also making noises when there were no balls in there. The cause was a loose opto emitter. I removed the supercharger cover and went into the switch test screen. Wiggling one of the opto emitters caused the switch to fire because the beam wasn’t quite making it through the hole across the channel. In fact several of the screws had started to back out. Tightened them back down again and all is well. Hope this simpler cause solves it for you. Maybe the shaker was the last straw getting those screws to start backing out?
Thanks for the tip but this isn't the issue. The supercharger noise is an issue when hitting the top pop bumper. I know it isn't the supercharger itself as it happens everytime I hit the pop.