You have a warranty, use it. Take it in, let Ford fix it.
Your 6th gear shouldn't grind, but then MT82s are known for being crap. Mine grinds every now and again, but usually when cold.
2012 GT Premium, Brembo PP, MT82, 3.73s, Blk/Blk. Bama 93R, Koni Yellow Rear Shocks, Hawk Ceramic pads, Luxurious & Plush Floor Mats