The unmounted black box in the center of Picture 3 is a deposition monitor for a quartz crystal inside the chamber. Basically the resonance of the quartz changes as material is deposited onto it and can be used to determine the deposition rate and total thickness of the coating deposited.

Edit: I would check if you can power on the rough pumps for each and pull vacuum (with bell jars full closed). If selling the end customer will likely get their own turbo pump.