what intake mod? I don't see how it could matter. If the issue is in the rear end, they'll look at the rear end. They probably won't even open the hood.
I drove my 03GT in with an IRS from a 99 cobra, cross braced subframe connectors, lowered, interior gutted, intake, X pipe, cat back and all kinda crud and my PITA dealer didn't even wink. Just replaced the tranny and clutch and sent me home. I don't think they'll care about a shiny CAI.
Near as I can tell, you've voided the warranty on any parts you've replaced and that's it. Until you do something silly like put a blower on it or nitrous, I wouldn't worry about it.
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