I am assuming you are talking about the warranty on the supercharger itself and not the car's warranty.
Most supercharger manufactuerers will only warranty the supercharger installed on a stock car with the supercharger companies canned tune. The issue is, most of the time, these tunes suck, and only have 4-5 lbs of boost. Because of this, pretty much everyone gets a custom tune, and smaller pulley's, which void the supercharger warranty.
In your situation, when you add things like headers, it requires a special tune voiding the warranty. Honestly...in my mind the works supercharger and warranty of any kind do not go togethor. When you go adding 150 HP..stuff will break if you use that power consistantly.
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