98'MustangGT, I asked my dealer about doing the same thing. They told me that it would only void the warranty on my gears--and not the rest of the car.
If your dealer is going to give you a hassle about making minor modifications like gears...
find another dealer!
I don't know what's available in MN, but if you can, try to find a dealership that is a licensed Motorsport dealer to handle your service. They are used to dealing with performance parts and are usually pretty cool about modifications (usually if you're happy, that means you will come back to buy more from them
).
I deal with Tommie Vaughn in Houston and they have never given me a hassle about modifications.
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2000 GT --
Black, 5sp, Mach460, Bassani CatBack & X-Pipe, MAC Cold Air, 70mm Tbody, Hurst Shifter
1966 Mustang Coupe --
Tahoe Turquoise, Pony Int, A-Code, C4 Auto
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scott@pearland.com