No, not stupid. Are you getting a check engine light? If you have an OBD code reader, you should look for the codes, to include "pending". The 2 coil packs bolt in place. So it's easy to tell if they are not in the right positions. It's also easy to push the boots over the plugs but not get solid contact with between the wire end and the tip of the plug. A missing cylinder will make it run rough, for sure. Also, any connector not completely seated can do the same if the ECU is being retarded when interpreting and "correcting" the bad signal. But I'd bet the rough running is likely associated with the plugs and wires... I vote for the wires. And don't forget the little connector that runs to the coils from the back of the valve cover. It's easy to overlook. That said, once you have it running again, there's a chance you might get a "fuel system lean" kind of code. That can happen if there's air leaking into the cross pipe or any area downstream from the MAF. I tell you all of this from experience... cuz I do that kind of stuff too. <img src="/forums/images/graemlins/shiner.gif" alt="" />