You would never run a PCV valve with a vacuum pump. The entire crankcase will have one opening that goes to the pump and thats it (so it can create a vacuum environment inside the crankcase).
The method you choose to vent your crankcase will have no bearing on Manifold vacuum. You're confusing crankcase pressure and manifold pressure. With a PCV valve you use the manifold to vent the crankcase, but this has no appreciable affect on the MAP. Any other method has no affect on MAP.
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