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Well are you referring to the intake manifold or the exhaust manifolds? If it's the intake its a vacuum leak. My Ranger 4.0L did the same thing after I took the plenum off to change the valve cover gasket. I found out it was EGR tube going to it. A very small vacuum leak will whistle for sure and really make the car run like shit. I suggest tearing it back down and change the gaskets and torque it correctly.
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