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Just one thing to keep in mind is the Roush supercharger upgrade voids any warranty from Ford on the motor or trans. That's the info I have got from the dealer and from Roush. If you DD your Raptor, this may at some point, be an issue. FYI.
I'm pretty sure if you add the full roush kit the roush components are 3/36 if installed by a dealer. Roush sells a power train warranty for an additional fee. If the truck is brand new and roush does the install it is a normal ford warranty.