Let me say from the start that I am no expert on anything mechanical... I have read on this site that after you install a CAI kit, the ECM needs time to re-learn the air/fuel mixture for optimum performance. If you immediately installed your SCT tuner, you may have selected a tune that the ECM perceives as too aggressive. I would un-install the SCT tuner and drive you truck for a few days to allow the ECM to complete the learning curve. Then re-install your SCT tuner.

If this is incorrect, please feel free to correct me.