The stock brakes will work just fine with the 31'' tires you have. I have 37'' tires on my 85 truck and the stock brakes work just fine, but i upgraded the brake booster and master cylinder. I pulled a duel diaphragm brake booster and master cylinder from an 89 two wheel drive toyota truck and swapped it into my truck, it improved my braking quite a bit. I am going to upgrade to vented rotors and V6 calipers in the future, so im starting to gather parts for the swap.

1986 Toyota 4Runner.

Solid Axle Swap, 5'' Lift, 37'' MTR`s, Duel Cases, Detroit Locker Rear, ARB High Pinion Front, 4.88 Gears, Cross Over Steering, Trail Gear Sliders, Addicted Off Road Front Bumper.