The only problem I ever had with the brakes on my 98 was when the tire dealer's help got carried away with the impact wrench and warped my rotors. The pads had 128,000 on them and had a lot left when I had to replace the Runner.

My 97 had the brakes pads replaced before I got it whatever brand they are they don't seem like they are lasting as well as the Toyota pads did on the 98.

I have an automatic but I usually downshift with the auto when I'm slowing down and let the engine do some of the work for the brakes.