When I asked my warranty company (United Car Care) about upgrades and repairs (I specifically asked about adding an aux input to the stereo), they basically said that as long as they're factory OEM quality and done by an ASE certified shop or dealership, then things should be covered.

You'd be safest if you used BMW OEM wheels/tires and exhaust.

Wait for your warranty to expire before going crazy with mods. Unless you want to risk things not being covered.

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2006 X5 4.4i
Sport package, summer package, cold weather package, DSP + Nav
Bought 2/14 with 73k miles