They replaced an axle is the only thing powertrain wiseBut have you had to have any powertrain warranty work done? The only thing I'd be nervous about would be blowing the engine or tranny (for any reason - wouldn't push for dumb power), and then I'd be more worried about Ford finding logging record of install/tune manipulation in the computer than the dealership.
Edit: seriously love your truck btw. I saved it to my inspiration folder a while back.
Some electronics bits have been corrected even though I had swapped modules
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