If you want to run normal aftermarket mustang wheels then you will run into fitment issues when using a recommended tire size (such as 245/45/17 on a 17x9) because of the offsets on all of the wheels. If your going with a 17x8 cobra wheel such as on a 98 cobra, my brother runs that and his wheels are dead on with the fender lip and don't rub.
-of coarse if your gonna run custom aftermarket wheels, it shouldn't be an issue, just get a larger positive offset. The only thing that is wider on that assembly are the axles, the housing, and internals are all the same. So for piece of mind you could get better aftermarket axles. I picked up a set of USA Alloy axles from summit racing for $200 shipped. And I love them.