Granted I'm only really familiar with the 3.0, but wouldn't at least one line go to the vacuum solenoid for the EGR? On my motor, there's a line that goes across/behind the intake manifold to the EGR solenoid, and then another line from that to the EGR valve itself. I don't know what lines you have pulled, but might not be a bad idea to check your Haynes/Chilton manual to see what vacuum lines might be missing.