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I am a new SHO owner I am wondering if I were to start doing some small mods to the car like a new tune, intake would that void my warranty or if need be change the tune back to original.
I would be careful of major mods especially powertrain related unless you can get in writing that the mod is certified by Ford Engineering. Welcome aboard by the way and while your at it define "Small Mods"?
Any performance mods technically void your powertrain warranty.
Some dealerships are more lenient than others, but if a major repair is done that requires a Ford Engineer to approve then you will most likely be paying for the repair and losing your remaining powertrain warranty.