I run 31''s. The factory brakes seem strong enough but they are surging so Thought I would see what a pain it is to upgrade since they must be close to toast.OEM is the way to go unless you're using very large tires. The 4Runner caliper mod doesn't gain any stopping power over stock and requires cutting up your dust shields. (Not a big deal if your truck is a rusty mess but will reduce the value of a clean one.)
If you've repaired the existing system with good quality parts and are still unhappy, you might consider using an FJ-62 (or 4Runner) vacuum booster. It will reduce the pedal pressure needed to lock up. If your brakes won't lock up 31" tires, fix them until they will.
There is a Tundra mod for people running 33+ tires, towing, or heavy loaded trucks. It is very expensive, requires changing all the brake components at once, and running 16" rims. It works great but I don't recommend it for your application.