Back to basics....have you triple checked that the valve cover gasket is fully seated, and that it's sitting on the head straight? It can take a few tries sometimes, and the VC gasket sometimes likes to move around while you are trying to get the valve cover into place.
I think you are referring to the PCV vents? There is a short rubber hose that goes from the valve cover to the intake manifold, and then a larger hose that goes from the valve cover to the top of the air cleaner. Otherwise I don't know what you are referring to off the top of my head.
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