First -- does that CAI require a tune? Many of them do, because the mass air flow metering section (tube) is larger diameter than stock, which means the tune must be adjusted, if not corrected the MAF (mass air flow) signals to the computer will be wrong (computer thinks less air is coming in than actually is coming in) and the car will run lean as a result.
Next -- what tune did you load from the SCT? Did you make the adjustment for the correct CAI, meaning the one that you have? Different intakes have different tube diameters and that is why you must use the right one, or one that has the same tube diameter as yours. I believe you can select/adjust the CAI in the tuner before you load the tune, but I haven't done it myself so not sure exactly how the device presents the choices. If you are using the tunes that come with the SCT, I have heard they are not very good, and I don't know which CAI's are supported. You probably need to get someone to write a tune for your car with the correct intake adjustments.
I would avoid driving it until the issue is corrrected, if you do drive it, go very easy.