I have stock wheels & tires, so there aren't any problems. A larger wheel & tire might require a deeper offset or rolling the inner fender lip. If you buy the wheels new from a good dealer, you can specifiy the extra offset when you place your order.
If I ever go to a 5 lug axle, I may have some problems locating 5 lug, 10.5" vented rotors for the rear. 94-98 axles will fit according to Matt90GT's site, so the axles won't be a problem.