Hi All. Longtime reader, first-time poster. Last night, I finally found the cause of the exact same problem. Like many surge sufferers have found, my throttle wasn't seating completely on the stop. Most times, it wasn't even off the stop enough to increase the idle perceptibly. Just a hair. Like, you probably couldn't even get one of those paper-thin shims in there. But, it was enough that with the brake pressed, she would start surging. It drove me crazy for about a year. I did all the things to chase it down. When I say "all the things," I mean ALL the things. I won't list them here.
When I finally found that the throttle wasn't seating, I thought the throttle body was sticky. So, I cleaned the **** out of it. It was super dirty, so it was needed, but it only "fixed" the surging for about two days.

Finally, last night, I realized (while working on something else) that my throttle cable was routed with one sweeping curve and one small/pinched curve. I mean, yeah, go ahead and haze me for that one. It's just sitting right there on top of the engine for everyone to see. It's so obvious that I just never thought about it. It was creating just enough tension/friction in that smaller curve that the springs couldn't get the plate to come down that last little bit. The linkage was also full of dust, causing the cable end to see a just touch of pushback when it was trying to wrap around the curve.

So, I balanced out the curves in the cable, made a nice, clean "S" shape, wire brushed the linkage, and hit the end of the cable with a little light grease. Boom. Done. No more surging.

Now, I'm no expert on these old computers, but it seems that they don't like the idea of throttle and brake at the same time. Apparently, doing so throws them into some kind of temper tantrum mode. Poor little First Gen 4Runners sound like they're sobbing when they get the surge going.