I have a buddy with the same 4Runner and he upgraded to later model brakes with bigger wheels and tires. I don't remember exactly what he did but I think the next generation of brakes can be retrofitted. They are an inch bigger and require the 17 inch rims rather than the 16 inch rims that these came with.
Yes thats what mine has stock, I'd still try the higher end EBC pads/rotors first, should be fine as your runner (I'd assume) is a good bit lighter.
