And with my Specter Ram Air Intake setup, I failed the visual inspection because I didn't have the O2 sensor plugged into the intake pipe where it should have been (the sensor wont reach the pre-cut hole in the pipe, but I'll be taking care of that later today today; I'll be drilling a 15mm hole into the straight section of the pipe where the sensor can reach). However, I successfully passed the Functional Check and Emissions Test, no problems.
The guy told me when I come back for the retest, I either have to produce paperwork that shows that the Specter intake is specifically designed for the car (which it isn't) and that it is all emissions legal (I assumed it was ok, the filter's box said so, and it's not the one that says "track use only", all in all, nothing I can really do); or just to be safe I should just put the OEM intake back in.
At the end of the day, I ended up putting the stock intake back in for the sake of the visual test, and had a retest done not too long ago, this time passing the visual inspection, and the Functional Check and Emissions Test with no problems.
So here's a tip to all you future smoggers out there: If you have an aftermarket intake and no paperwork to prove that its emissions legal (the case of most Specter intake people, correct me if I'm wrong), put the stock intake in before you go to have your car tested.
All in all, I spent $110 on a smog test