Once, mine was running rough and I checked the plug wires to find one of them was loose. I think I was running on 3 cylinders. Now I'm real careful to make sure they click all the way down.
Otherwise, why not check a stock filter? Its a relatively cheap fix.
I assume you have checked to make sure the plugs are tight in the holes also. Sometimes, if you don't get a good crush on the washer, the plugs will loosen up and suck air/blow gas, causing it to run crappy.