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Hello, if the upper intake manifold is plastic and you feel the noise coming from inside there they had issues with the upper intake plenum chamber seperating and causing a knocking noise so you can replace the plenum and it should take care of the noise. Trans fluid in the oil shouldnt affect too much depending on the amount put in. It acts like a cleaner inside the engine and will break up sludge deposits. So draining the oil and changing the filter will help that. Far as the running rough with raining would mostlikely be an issue with either a bad ignition wire or problem with the camshaft or crankshaft sensor which may store codes when checked with a scan tool.