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If you get off road and start pushing the limits of the Raptor, i.e., high speed jumps, etc., you could bend the frame from excessive impact at the bump stop.
I would do a tuner first thing. Just the change in shift patterns makes it a much more enjoyable DD. I got mine from 5 Star (vendor on here) and am very pleased or you could probably find one in the Garage Sale or Ebay/Craigslist threads.
Wish I knew more about tuners. Not knowing the benefits doesn't help the case to purchase
Personally, I'd wait until you did CAI and exhaust at the same time if you want a tuner. I don't think they add much to a stock setup but with a free flowing intake and exhaust, you can squeak out some power.
I'm hesitant to do a tune while I'm under warranty. Maybe once I get closer to the end of the warranty I'll fell different though.
I've driven one with a 5star tune, airaid intake and magnaflow exhaust. It didn't feel much faster than stock but the transmission shifting was much improved. For now, I just use tow/haul mode when I want to drive agressively.