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I've had headers on numerous cars and never had a warranty issue. Same with CAI's.
Couple of red flags to avoid - Don't show up for warranty work with an aftermarket calibration in the ECM. If you want to do tuning, research that what you are doing can be reversed. Power adders like superchargers... forget about the warranty. Same with mechanical mods like cams... warranty, done.
Exhaust and intake should be more than fine. Best thing to do also is stop by your dealer that will be doing the service work and ask if you can run a couple questions past the Service Manager. Tell him/her what you would like to do to get their opinion of what they think of your ideas. Most will be perfectly fine. If someone seems to be a bit prickish about mods, then you will know to show up 100% stock if you need warranty work. So just keep everything you take off handy for a reinstall someday if needed. I.E. don't sell the cats to a junk yard.
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