Not all options for extremely modifying your car are going to be emissions legal, you just do what works for you. Everything can't be 100% legal in all 50 states.
For those who are reading and don't know, AEM is an incredible system, but you're going to pay a good amount of money for it. But once you have it, you have great tuning capability.
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JDLAutoDesign is that Series 2 or EMS4? I'm assuming you didn't go with Infinity, lol