Previously I though I had broken my pump.
So the pump is back from repairs. But the strange thing is when Pfeiffer received it, they said it was working fine! Although I did manage to knock the rotor out of balance and it needed fresh oil. Here is the pump capped with a blank conflat running at full speed. GOOD.
But the problem was never the pump! The problem is a gross leak in the vacuum chamber.
Once I attach the pump to the chamber, the pump won’t spin up… indicating a gross vacuum leak.
The copper gaskets are all new, and I even got the torque wrench out to make sure the conflats were tight enough.
I can’t hear any hissing.
How do I troubleshoot this…
Here is a good overview on leak detection.
UPDATE:
I though I head a hiss near the bellows. So I tested just the bellows and it’s working fine. So the leak is somewhere in the chamber.
Prometheus Fusion Perfection 
use the bike tire method: immerse in water, pump in air, look for bubbles.
There is no need to put into water. With a brush put a little soapy water where do you want to check and look for bubbles
But this would require pressurizing the chamber, not vacuuming.
in the updated picture, it does not look like you have the butterfly valve installed.
We know that you had that valve apart just propr to the incident, and it would reside just above the bellows. Did you have the butterfly installed when you were testing, and thought you heard a shistle?.
Try setting it up with the adition of the butterfly valve.
I’m not using the butterfly value at all for the vacuum check. My feeling is you want to have as few parts as possible
How do you torque down your fittings? Do you just go in a circle?
I’m just a simple mechanic, but I know that you can warp things if you don’t torque them down in the right order.
For your round fittings, go in a star pattern, that makes sure you don’t push a warped spot to one side, not sealing it.