if you plan to spend time in the desert, I'd recommend the volant intake with the donaldson filter ( its a dry tractor filter that is probably the best on the market for heavy dust). The cobb is a great street filter that helps make good power with a tune, but it cakes heavily in the desert.
I run svc traction bars. I love them and would only remove them if i was linking my truck.
If you have the budget, I'd skip the collars and go straight to a shock upgrade. For trucks that will maintain stock width in the front and want to maintain the bed integrity, I like the ICON RXT setup the best. I've watched the expedition x offroad guys HAMMER the icon setup ( including Tom Wayes. If you don't know who he is, look him up. He's a pro ultra 4 driver and is a consummate madman! )
as far as the tune, I had mpt, then cobb, then went back to mpt. with mpt the trans shifts like a well oiled sequential during acceleration. The cobb OTS tune introduced an ever so slight lag when stabbing the gas. The mpt is a bit better about it.
My happy place on exhaust is SPD downpipes, borla resonator and a wraith offroad high clearance exhaust.
keep in mind though, a positive comment for a gen2 exhaust is generally " wow this is the first gen2 that i don't hate the exhaust note on."