Yes they will honor the factory warrenty if installed by a authorized installer. Just like any other Mustang, install any after market part that causes failure - usually not covered. You guys get too critical of chioce of built. They picked a base, if they had chosen a premium, some would ***** about that. Unless you are going to be beating the car on a track, the extra cooling not needed or the big brakes, you would start out with a Boss for the suspenson, brakes and cooling. Do that would bring you right up to the Roush Stage 3. The sound and build is just like a lot of you are doing now.
2015 Stage 3 Roush
'66' Ranchero w/almost done 302 T-5 swap
2000 4x4 Ranger
2003 4x2 Ranger
'69' Fairlane Cobra, 428 4-speed waiting for work