Generally speaking (outside California) you are required to have the same year or newer engine along with retaining and integrating both the engine (i.e. egr, pcv, etc.) and chassis (i.e. evap, cats, etc.) emission equipment. On these newer engines it really isn't that difficult as most of it is all integral to the engine anyway. It usually entails running all 4 O2 sensors, running cats and integrating the EVAP system. The best thing is to check with the local referee station to be sure. Sometimes the local referee station doesn't even have it right and you'll have to look at the local laws directly. California adds a whole new level of difficulty as they get more specific with what transmission can be used and all parts have to be CARB certified.
This JK doesn't have to meet emissions in Cache County but it will be set up to pass anywhere but CA.