glasman,
It sounds like there are only two circuits on the downstream side of the intake manifold, the hydra-vac and the two speed rear end.
I have never seen the check valve for the hydra-vac fail before, but the diaphragm in the hydra-vac might be bad.
If you start the rig with all hoses connected, then shut it off, you should have a 'powered' pump or two left in the brake system.
If you do, this means the system is vacuum tight, everything is working and the problem probably lies with the vacuum two speed shifter.
The conventional method to find a vacuum leak is with some type of spray can containing something more volatile than gas...like carburetor cleaner or brake-kleen. When you squirt this on a fitting or connection that is leaking, the material is drawn into the engine and you will notice a rise in RPM.
Using this method you don't have to have a clear visual path to see bubbles disappear.
Stuart
