Check your fuel pressure. If it is to high you will not pass the emissions test. Have you tried a cylinder balance test? Maybe one or more of the injectors are leaking and/or have a poor spray pattern. With the engine running disconnect one injector connector at a time noting the RPM of the engine. If each cylinder is putting out the same power then the RPM drop will be the same no matter which injector is disabled. The one cylinder whose rpm does not drop as much is the culprit. When you pulled the sparkplugs did you notice if they were all of the same color? If there where any that where a light tan while the others were black, the light tan one is in the cylinder that is not running right. Another thought, spray some water or carb cleaner around the intake manifold gasket area with the engine running and see if the RPM's change. If it does then the gasket is leaking and needs to be replaced. Good luck!