I sold my stock wheels and stock lug nuts. I still have the factory spare wheel/tire, but no factory lug nuts. In an emergency, would aftermarket lug nuts work on the stock 4Runner wheels? I had the 18" Limited wheels, now on ATX Mojave's.
Chances are the aftermarket lug nuts will still catch the lip on the stock wheel, and might even center it okay. It's not recommended to run tapered lug nuts on a hub centered wheel with flats at all, but would it work in a pinch? Probably. I have the same issue as you except I kept some stock lug nuts.