Lets see if we can open up a whole can of worms here...
First things first, unless you're racing the 4Runner or have a 12 mile descent followed by an immediate stop-and-park situation, it is VERY unlikely that you're warping your rotors. Warping occurs when the heat within the rotor approaches the annealing temperature and is then allowed to cool quickly or non-uniformly. That temperature is in excess of 1000°F for most cast iron alloys. If your rotors were getting that hot you would DEFINITELY notice.
The more likely scenario here is what I call "stiction" between the pad and rotor at lower temperatures (but still hot temperatures). Basically, your rotors get "hot" during normal operation and the compounds in your brake pads, which are designed to create friction but keep sliding freely, "stick" to the rotor surface microscopically. That material then continues to get pounded by the brake pad every time the rotor spins under it with the brake applied creating "carbides", or really really hard spots, on the surface of the rotor. THAT is what you feel when you hit the brakes and feel a "wobble" in the vehicle. If you hit the brakes and feel the wobble in the seat but NOT in the steering wheel, the it is likely your rear rotors that are in question. If you feel it in the steering wheel immediately, it is likely your front rotors but could possibly be all four. This has been confirmed tons of times by machinists (myself included) who load their rotors into a lathe to machine the "warp" out of them only to find that they are still nearly perfectly flat when inspected with a dial-indicator. The temporary fix is the same in either case and requires machining or replacement of the rotors.
Now, what the hell do we do about this? There is not a perfectly straight forward answer to this question because it happens with nearly all rotor and brake pad types, but using high quality ceramic or semi-ceramic brake pads on high quality rotors seems to be the best bet for minimizing it. The other thing tends to be driving habits. People who brake hard and fast and don't let the rotors "slip" a little as they come to a stop experience this more often than people who roll to a stop slowly. Hard and fast results in more opportunity for those "carbides" to stick to the rotor whereas they are less likely to adhere when there is slipping occurring between the pads and rotors.
The other thing that I hesitate to recommend, but I have had good luck with, is using "Stop Squeal" (Amazon) on your brake pads. It seems to add another compound to the pads that helps to prevent sticking. For some people, adding any third party products to brake pads or rotors is taboo. This is up to you to decide for yourself. I used to have this issue all the time on smaller faster cars. It happens much less on the 4Runner, but it has still happened to me. I am still on OEM rotors and pads but I will likely switch to "Power Stop" Tow Duty pads and rotors when the time comes. I have had better luck with them than any other brake company I have ever used. Hopefully some of that proves useful to you and you're able to find a combination of parts and driving style that works for you.