[gunman0]

You can see if there is a bad check valve for the secondary system by pulling the vacuum line to the middle of the driver's side of the plenum. Put your finger over it and see if the vac pump stops running every 15 seconds. If so, you can just throw another check valve there as a quick fix until the next time you pull the plenum.

I don't think a secondary vacuum leak would cause the low rpm miss like you describe. Also the fact that it picks up power over 3000 rpm seems to negate that as being a major problem.