The disa flap should not cause the rough running/missfiring. It sounds like you have a big vacuum leak, most likely at the oil separater/crankcase vent valve. That is the one undder the intake manifold, towards the front... near the oil filter housing. Thats what the big plastic hose coming off of the front corner of your valve cover goes to under the intake.

When that part fails, it gives a big vacuum leak and burns more oil. With the engine running at idle, open the oil cap on the valve cover. It is supposed to have a slight vacuum, but if it feels like a vacuum cleaner is sucking on it... that narrows it down to just that oil separator cyclone valve.

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2003 4.6is