Mods can only void your warranty if the dealer "proves" your mod caused said problem - though there is much discussion on this issue, search the forum.
As for your mod - theres a big difference in price between an cold air intake and a cat-back exhaust so if your decision right now is driven by price, then consider that the Gen3 are less than half the price of the FI cat-back.
If you are doing the install yourself, intake is easier to do.
Performance wise, they will be about the same. The first bolt-on modification you do has been shown to produce the most power (15-20ish) whether its an intake, exhaust, high flow cats, whatever. Then each subsequent mod adds about 5hp or so. These are approx numbers.
The best bang for your buck is HFCs or test pipes, HFCs being the preferred option because they are quieter and you still will have cats as opposed to test pipes which eliminate catalytic converters altogether. Arguable going forced induction (twin turbo or supercharger) is a better bang for your buck, but youre spending alot more bucks for alot more bang.
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