If your pump is worn, or defective it may still run just not move enough air to make the ECM happy. Also chek your hoses going to/from the pump. Those pumps are mounts low on the car and tend to corrode and get water in them from years of use.

 

ok so the update is.... i checked the dv and it holds vacuum, i had replaced the hose going to the dv from the solenoid, when i worked on my head. I noticed that that hose on the dv side didn't have a clamp on it, even though it was a tight fit, so i put a clamp on it. Also applied 12v to my pump, and it ran well, strong and with no hick ups. Noticed that a vacuum hose on the front of the intake manifold looked nasty, not sure if it was torn or not, but replaced anyways. I also replaced the egr solenoid yesterday so only time will tell as i cleared my codes. If this doesnt work my next guess would be just to replace my combi valve even though it sounded perfectly fine, and held vacuum like the new one did. Any other suggestions? I have checked fuses, all good.

 

More likely than not the combi valves on the back of the head are starting to get clogged with carbon. Usuallly removing them and cleaning them will fix the problem. This of course is assuming the pump is operating properly and the valves and their control circuit are opening and there is no leakage in the system.