To put your mind at ease over the pump, you can disconnect the vacuum line at the coupling where it goes under the plenum, and with the ignition switch "ON", the pump should start running and continue to run. By putting your thumb over the end of the vacuum line, the pump should shut off in about a second or so. If the pump quits before you plug the tube with your (thumb), then the pump and associated switch come under suspicion.
However, as mentioned, the pump only provides initial vacuum charge at start-up and will sustain vacuum under prolonged WOT situations. Otherwise, the plenum vacuum will maintain the vacuum and actuate the secondaries and the pump remains shut down.
If the test with your thumb proves the pump is functioning properly, it can also be assumed the integrity of the vacuum circuit up to the vacuum solenoid is not leaking (or the pump would not be shutting off). (see below)
Did you get an SES light when the secondaries should have opened?
If YES, then there is a vacuum circuit failure which may include the vacuum solenoid and all components up to and including the differential pressure switch. A miti-vac will be helpful to isolate a vacuum leak, if there is one. (Make sure the secondary actuators operate freely. As mentioned many times before, some actuators were installed incorrectly at the factory, resulting in the actuator rod pulling at a angle instead of in line with the secondary linkage.) If there is no vacuum leak, the differential pressure switch can be dismissed too (the diff. pressure switch signaled "no vacuum" and consequently the SES light, and the vacuum solenoid and it's connection are next (and last).
If NO SES light then the vacuum circuit integrity is intact, and the secondary actuators come under suspicion. A miti-vac pump will quickly show you if you have a failure to actuate!
Just so much one can do w/o seeing what is going on. But, hopefully this will get ya started. Personally, I opted to toss the entire secondary headache - vacuum lines, check valves, pumps, actuators, etc, etc, including the throttle plates and all hardware. Unless you're running an NCRS car, you'll never miss 'em. In fact, you may discover you like the responsiveness and the freedom from every worrying about it again. But, you'll need a chip that has been prepped for running sans secondaries; Marc Haibeck can accomodate. I believe you won't regret taking the plunge! (Most all of the FBI gang is running secondary free, and the number continues to grow!)
Just an aside... When first turning the ignition switch to on, and before rolling it over to actuate the starter, you should see the SES (among other) lights come on for a second or two - part of the ECM and bulb test. If there is no SES then, well I would want to get that fixed right away!
This would be a good stopping point. Continuing to play "what if" without specific additional results from troubleshooting will just lead to that overwhelming morass of confusion...
Check it out and get back!
FWIW,
P.