A vacuum boost pump is designed to assist the manifold vacuum, not be used instead of it. I've seen people install a jumper line between the ports instead of blocking them off, and run like normal if they want to disable the vacuum boost. I suspect the problem with blocking the flow is that a vacuum is being formed which keeps the fuel section of the pump from working right. Either leave the ports unblocked, or install short sections of vacuum line and hide the open ends around behind the engine or something.
Jerry

"It is better to be silent and be thought a fool than to speak and eliminate all doubt!" - Abraham Lincoln
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