I do not turn off any emissions systems in the tune. The stock air intake system can still be retained up to about 700-750RWHP. I don't see any problems with you passing.
The FRPP Cai has an EO number, I have one. The good news is it sounds like Justin's Tune will pass sniffer, most custom tunes usually do. The Visual inspection is the question. Currently no test until the 6th year