Craig, the leak sure can cause the problems you are having. The engine is sucking air from the leak causing a lean condition. The best way to fix the leak is to have the intake and exhaust machined or ground. I bolted both manifolds together with a new gasket using the three bolts, then took it to the local shop and had them grind the flange side even. It was pretty cheap and didn't take but a few minutes. I can now remove and install with out leaks. The truck ran much better after the grinding.
You can try loosening all the bolts and adding some sealer around the intake ports, adding some lube to the nuts and spacers so they turn easyer also helps. Tighten the bolts on the head first, once they are tight, snug up the three going to the exhaust manifold. If you will notice, some of the bolts going in the head are higher then the others, try tightening them first so its not drooping down. Also hold it up so the bolts don't have to try and lift the whole assembly up flat to the head.
With a mismatched intake and exhaust manifold, you may have a hard time getting them to seal, I know I did. Joe
Last edited by Joe H; 09/17/2008 5:20 PM.