I've been defected 3 times, EPA(ed) 2 times and had my car impounded once. However, my car is far from "stock looking."
Anyways, if a cop feels "in his authority" and within reasonable that what you have on or in your car is illegal and could/can cause the car to act in a way that is deemed unsafe for you to drive or dangerous towards others etc, he/she has the right to inspect your car and there's nothing you can say or do. Whatever they dish out you must cop it sweet...you have the right to go to court to fight the fine, but most likely you will lose so why bother.
You will get the EPA later...it usually comes after 1-2 months. You will get it and it will be a pain to get your car cleared, but this is what you expect if you drive a JDM sports car. Nothing more I can say bro, just cop it sweet and just hope you get better luck next time.
Sorry to hear though.