Most Tuners turn off the rear O2 sensors to keep them from changing the mixture.
Unfortunately you cant pass emissions with them off. You cant complete the drive cycle test for the Cats.
Since you cant run the Stock Tune with a CAI (Any worth buying that is) you need to reinstall the stock setup or use Mil Eliminators.
The Mil Eliminators simulate the rear O2's are reading "Good" at all times. So they wont effect the fuel.
So that way the tuner can turn "On" the rear O2's and not be effected by them trying to lean or richen the mixture.
The tune needs to be adjusted to turn the sensors back on, even though they wont effect anything.
So that way the PCM reports they are operative and good for emissions testing.
They are about 8 inches long and go inline between the sensor and the harness.
I got them for emissions, but my Tuner made a tune for emissions testing for me (It is a secret what he does) after I got them, so I never needed them.
Oh and totally Off Road Use Only

The EPA cracked down on Mil Eliminator manufactures recently and they are hard to get now.
Richard Sr.