On my old motor, I always failed with my short ram intake on, why? I seriously don't have a dang clue... put the factory air-box, resonators, and etc, reset the ECU and I passed with flying colors. You might want to try using those additives for your gas, they clean up everything inside; but don't get the bootleg brands.
Shockingly, and with a sigh of relief, my new motor passed inspections without any problems- B16 CAI/E...