There should be a vacuum diagram on your hood, If not then look on google search for it and your bound to find it. BUT, I have one more question for you that I need to know before I can tell you what to do.
On my swap, I swapped an LS motor, But I put a skunk 2 manifold on it before i put the motor in the car. Plus I have a bigger throttle body on mine so therefore that eliminated 2 Of the vacuum hoses. Then I took vacuum hose #21(there all numbered) and T'ed It with the hose that goes to the back of the manifold, So there was 2 going into 1. My question is, is the manifold stock???? If so you probably just didnt hook up a vacuum line or you got 1 ran wrong. Check it out, Look under the hood for that diagram. If not look on like, CRXSI.com or CRX.org.