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The aux water pump is located below the washer fluid reservoir on the diesels. Follow the heater hoses in that area. If the pump is missing, someone may have bypassed it. Normally the hose routes from the firewall, to the pump below the reservoir, and back up to the pipe at the intake manifold near the throttle cable area.
The wiring to the 7-port manifold comes from the pushbutton control unit, which controls the manifold, telling it which vacuum ports to open or close.
If the pushbutton unit moves the dual-chambered pods, it's doing SOMETHING. Remember the other functions (opening single-chambered pods) depends on both the buttons pressed, temperature selected on the wheel, AND cabin temperature from the sensor in the dome light assembly. If you set the desired temp to max cold (click the detent on the wheel) this should open the center vent pod.
You'll have to start going through the factory manual which describes operation in various scenarios. Here's a link:
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