MadMaxx
Full Access Member
A lot of people run tunes, but not many use CAIs on our trucks due to the CELs they cause. If the AFE CAI is new like the OP mentioned, I would remove it first, clear the codes and see if the problems persist before adding cleaners.
CAIs provide very little benefit on a Raptor other than sound and bling under the hood.
I run the Agency Power Intake on mine and have no CEL, and it doesn't use the stupid Vent Tube either. But yea, like you said, many other Intakes on these truck can throw the CEL and cause other issues.