First, If you pulled the upper intake plenumn, They have preformed "o" ring style gaskets, the other common intake leak on the DOHC motor is the PCV hose assy. It's very hard to hear a vacuum leak on these motors because they have a plastic upper plenumn and we call it a loud intake, meaning they all sound like an intake leak because they are noisy and sound like a vacuum leak.
Was it misfiring? another issue that Fords had was an injector staying open, dumping fuel into the intake.
One trick to see if the injectors are firing, take a long screwdriver and hold one end to the injector and the other end to your ear, you should hear an amplified "ticking" noise...if not you have a shorted fuel injector.