Link and ItchyDong gave good advice.
The CAI is unlikely to be the culprit here. The sensor you installed in your CAI is an intake air temp (IAT) sensor. The PCM uses it plus the manifold absolute pressure (MAP) sensor to calculate the air density. It isn't going to be tricked into running lean (which can be an issue with MAF sensors), though I think the sensor in the intake manifold after the throttle body like the 04 and earlier is a little more accurate for the way these reverse flow engines like to heat the intake air at low speeds/loads.
As mentioned elsewhere, the precats do have a tendency to disintegrate themselves with time without a cause and it's quite possible it is just that. Many people replace them and have no further issues.
However bad O2 sensors, especially the 2 above the precats, a small vacuum leak at a cracked fuel injector O-ring, a small exhaust leak at the precat/manifold junction could result in the fuel trims being off, but not enough to throw codes.
You can monitor these in an app like Torque with a bluetooth ODBII scan tool. Or you can fully log them on a drive with more sophisticated tools like VCM Editor from HPTuners or a number of shop scan tools.
These vehicles are picky about their 4x O2 sensors and only like the NTK (NGK) ones specified for their designated position. You can find that part list easy enough. If you have any Bosch or other sensors in there, I'd go back to the NTK ones.