The CAI gets iffy. While it SHOULDN'T have any effect on the warranty, if there are any engine issues down the road, it's a lot easier for them to point their finger at the intake and blame that, than it is for them to do it on a catback. And while you can fight it, it's still a fight, which itself is a PITA.
Heck I've even had the dealer blame my muffler on my last truck. I was getting a ticking noise, I wanted them to check the plugs incase one was ready to spit (2000 2v 5.4 notorious for spitting plugs), and they told me that the back pressure from my aftermarket muffler was probably causing an exhaust leak up stream making the ticking noise, and I should put a stock muffler back on to remove the restriction. I said are you f'ing serious? My straight through 14" magnaflow muffler that you can SEE striaght through, is more restrictive than that 24" long UPS truck sized muffler I replaced? I don't think so lol. Then he recommended i replace my spark plug wires while it was in if they were going to check plugs. I just said give me my keys back, my truck is a 5.4 and it has COPS, not plug wires, I'll do my business elsewhere.
Needless to say, I'm avoiding the headache and keeping the stock intake for another 2 years till my warranty is up. I'll do other mods in the mean time, and the day my warranty expires I'll buy my truck a present of an intake and tune lol