Very good news! Keep plugging at the vacuum lines and it'll fall into place.
I printed out some vacuum schematics and colored in each "leg" of the circuits as I tested them. It helped me keep track of which lines I had checked. I had a couple of loose check valves and a bad fresh air element. Mine worked fine with both of the fresh air element lines plugged.
It helped me to separate the lines so I could see what was going on:
It also helped to use a little vacuum connector on the vac pump to check circuits:
I also found a leak in the servo vacuum switch which was screwing up my center vent flappage:
The Medusa like hoses were leaking so I replaced them...
Maybe this will help a little.