Ford is actually quite clear with their position on warranty (see manual). They will not void your warranty for any modification; however they may refuse to cover something if a component has failed due to your modification.
As far APS kits go, if your going to go a stage 2 kit, then you need to be prepared to cover (yourself) possible transmission upgrades or clutches etc as a minimum. They 'should' hold up for stage 2 (depending on driving style
), but best be willing and ready none the less. That way you will enjoy the experience and not worry about it. If you go the stage 3, then these things are definite items that will need addressing out of your own pocket.