Then what I would do next is learn about how each section of the vacuum system works - what each gizmo using vacuum does - learn when things are switched on/off.

With that knowledge, you could then disconnect and plug certain portions of the vacuum system, then see if the problem goes away or not.

For example maybe a line in the engine compartment goes to the climate control system inside the car. That could be disconnected in the engine compartment, climate control turned off, then see if the problem goes away or not.