Just had my engine swapped (for a wrecker engine, old one had bad rings) and it appears the guy that did it for me screwed up the vacuum lines.
he had the fuel regulator line hooked upto the bypass valve and the wastegate line strait to the manifold. there is also a line from an actuator at the at the front of the manafold just tucked under.
I have found a couple of diagrams online but they both mention a black tee and a blue tee, both seem to be missing.