I would make sure all the sparkplug wires are clipped in place.
Do you have the stock air filter or an aftermarket? Does this intermittnet problem have any thing to do with the weather? is so and you have an aftermarket air filter like a KKM then theres the possibility of water entering the induction system and causing rough running.
would the coolant temp. sensor have anything to do with rough running?
what about a dirty EGR, where sometimes the valve doesn't seat allowing too much exhaust to flow into the induction system.
