It's interesting that a production rig designed to run in the desert needs a suspension upgrade but it is what it is (you don’t want the “bent frame issue” to come into play). If you’re going to be beating your rig up pretty hard, better go with the upgrade. I would get the tune for sure but if you want a better sound then the CAI and exhaust would be good as well but performance wise, I’m not sure how big of a difference those two mods will make. I think they are mostly for show and not so much for go, at least where price to performance increase ratio is concerned.
Wheels and tires are a personal choice and opinions very widely. Lots of guys are running Methods and they look pretty good but your rig will look a lot like every other Raptor running them unless you do something different with the finish.
It’s all about what you want and what you like because it’s you’re Raptor, I sometimes have a hard time understanding the mentality of people when I read threads like this, it’s YOU’RE ride man, who cares what everybody else has to say about it???
Good luck...