In order for a manufacturer to void your factory warranty the Aftermarket Part must be proven to cause the failure of the defective part. That's according to the Magnisun-Moss act(hope I spelled it right). I've worked at car dealers for a long time so I know. For example if you have pulleys on your car and your alternator takes a crap. They are going to blame the pulleys for spinning the alternetor slower. The only thing that gets voided with gears is the differnetial assembely, Carrier, bearings, axles,etc...
Gears don't change the power output of the motor or exceed manufaturer guide lines so you can get away with those depending on the dealer. I know from personal experience. There are a few huge things that will void your warranty supercharger(except for steeda at an authorized Steeda dealer), Turbocharger, Nitrous, and a chip(except for steeda na tune at Steeda dealer). I have seen motor claims not only at Ford, but at Chevy for aftermarket computer chips. With all the new cars being electricaly contrlled this is one thing they look for. A chip modifies the manufacturer's set guide lines, changind A/F ratio, timing, shift points, raising top speed limiter, and even raising the red line. Hope that this helps a little.