Did you check the injectors? Start the car and let it run for a few min. See if the idle drops to around 550 where it should be. Then pull the plug off one injector at a time. If the rough idle or the misfire stays the same when you pull the connector off the injector, then something is wrong with that one. If you pull the connector off and the idle gets worse, then that one is fine. Do that one at a time with each injector and each coil. That will tell you which one is the culprit. Now once you find the problem cylinder, take the coil, plug, and injector out and switch it with a different cylinder coil, injector, and plug. Then repeat the test. If the problem stays in the same cylinder, then it is a wiring problem or you have mechanical failure like a valve or piston. If it follows the injector, plug, and coil, then one of those is the problem. So once you get to that point you have to swap out the coil, or the injector, or the plug one at a time with a different cylinder. If you swap the coils and the problem stays in the same cylinder, then it is down to the injector and/or plug. That is how you narrow it down. It should only take like 10-20 min.
