Check the firing order with the firing order diagram that I have uploaded, and if that does not solve the problem then remove the spark plugs and be certain that there is an even spark plug gap between all of the spark plugs, (see the emission label under the hood for the correct spark plug gap) and be certain that there is not any split-fire or multi-fire spark plugs installed in the engine, because those plugs will not work with an OBD-II system, and a random mis-fire is the least that they will cause if installed in an OBD-II controlled vehicle.
I would think bad firing order fist...if you are sure that is correct, did you pull any of the wire out of the boots? also did you drop any of the plugs? it will run rough if you cracked a plug or closed over a plug gap. re-check the order.
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