Well, there's a lot to consider. The runner is heavier than the taco, and rotor warp has been a big gripe. Since it's an '01 runner it has the 16" wheels, so you could swap over to the tundra brakes, with larger rotors & pads. Of course OEM seems to be the brand of choice, and brembo rotors. From what others have expressed, I wouldn't worry about the whole drilled & slotted stuff. As for other brands? I've been satisfied with performace friction pads, but I don't get caught up in all the hype.
For trial & error purposes, could get your rotors turned, new pads, and go from there. Go back up to Yosemite (that would just be horrible
), see if it's better.
Personally I noticed a change going to stainless braided lines, flushing the system and some synthetic fluid. May also check that the rear drums are adjusted (do you ever use the e-brake?), maybe check the drum pads. I should probably do my brakes, just been messing with other stuff.