I have an AFE CAI as well for the 4.7L. When I installed mine I reset the computer by disconnecting the negative battery cable while I worked on it.
I think the directions even indicated to do this so the computer would relearn the new intake.
Also, for me at least, I saw a slight improvement in mpg and noticed better throttle response.
2006 Commander, 4.7L, QT2, Dark Khaki, - RR 2.25" lift in front, OME HD springs rear, 265/70 Goodyear Wrangler Duratrac (no spacers, original wheels), OME shocks in the rear, Bilstein HD front struts, 4xguard: front guard, belly guard, side guard 2, & rear sliders. Skid plate group with front two hooks, heavy duty tow package, AFE CAI (dry filter)