Congrats on the new truck. I wanted to get a Citadel too, but the CrewLux with all the trimmings had the better deal. Despite some of the niceties on the Citadel, if you test drove a CrewLux, that may be some of the differences you are seeing. The CrewLux comes with a Garmin nav which is a little nicer than the unit in the Citadel. The Citadel nav (I believe) is better integrated with the voice command system, but isn't as refined a unit as the Garmin in it's basic functions (like the speed limit). I'm not as certain, but I think the hard drive is the same way. The CrewLux with the Garmin has the 30G, the Citadel only 11G.
You got the nicer leather, cooled seats, and heated steering wheel (all things I wanted) and some additional chrome on the exterior, but you don't have the Garmin nav with the larger HD. As for the check engine light, make sure your gas cap is secure. Otherwise, it's definitely a trip to the dealer. Regardless, it's a great driving truck, and you will continue to enjoy it more and more.