I am starting to see a number of posts here and on other forums as well by people who have installed a CAI and are seeing a CEL (generally MAS sensor related) and are also seeing a degradation of performance almost immediately. Most often, but not always, people will also see a similar effect when installing a tuner.
So here is a tip.
Before installing your CAI, reset your PCM or simply disconnect your battery while performing the CAI installation. This should be long enough in most cases to "wipe out" the memory stored in the PCM. Also, this WILL NOT erase the aftermarket tune.
Most tuners, especially in their "Performance Mode" advance the timing, and as such, the PCM is running a slightly leaner (but still well within spec) mixture. The addition of the CAI will increase air/flow and further add to this lean state, often resulting in enough of a change to cause a CEL to come on as well as worse performance. Even if you do not see a CEL, the added influx of air detected by the sensor will kinda throw the PCM for a loop as it attempts to adjust values to it based on the information stored from thousands of miles driving without the CAI.
The problem is, a PCM by virtue of it's programming, will attempt to "balance out" what it is being told by the sensors with ALL the past information it has gathered either since day one or the last time it is reset. It will eventually make adjustments to the air/fuel mixture and the problem will go away. But this can, in many instances, take a lot of time over many miles.
By resetting the PCM there is none of that "learned" information in the PCM for it to rely on and as a result, the PCM will begin proper adjustments to your mix immediately.
I hope this tip helps.

Hammer...