Just so everyone knows.... I think part of my problem with my 98 4Runner was the wrong pads. There is an "upgraded" pad available from Toyota, that in conjunction with new rotors (Bendix), has completely eliminated the brake pulsing that I was experiencing. I was totally ready to upgrade the calipers and rotors to Tundra (pre TSB), but then someone at the local brake shop asked if I had tried the OEM upgraded pads. I replied that I hadn't. He said something like.... Look, if Toyota went to the trouble of making an "upgraded" pad, to evidently address a problem, wouldn't you like to try that before you go and completely redesign the braking system with parts that may or may not have been designed to work together? I figured, it couldn't cost much time or money to try it, and lo and behold it works.
I got the pads from CruiserDan, took about 40 minutes to replace pads and rotors, and it stops like a dream. I'll try to dig up the part number for the pads and post it here in case anyone else wants to go that route.
Luke