Just wanted to chime in since running across this post saved me hours. It is long so sorry but wanted to do a full brain dump in case it saves anyone else time or sanity.
99 4runner Ltd 210k miles. Love this thing...
My symptoms were that when I hit unlock on the key fob all of a sudden it would kind of half chirp one time, unlock the driver door but that was it. A second press on the remote did nothing.
If I hit the button on the dash to roll down the back glass the whole set of dash lights would just kind of flash a bit. Enough to make me think I might be crazy for seeing it.
Back glass would not roll down with keyless.
It came out of nowhere. One day it worked the next it did not.
Found this post and thought, ah what the hell. I kind of massaged the wiring loom you see when you open the rear hatch that has all the wires going into the tailgate. Ah ha!! Everything worked.
Well except that after that on my first drive I noticed my keyless worked but my speedometer died, ABS light came on, had to use shiftlock override to get into gear, and my check engine lite came on. Hmm, what have I done now.
Massaged the wiring loom again and now my fix stopped working. Took the boot off of the wiring loom and found two wires completely broken in half. Patched those and keyless came back.
Ended up replacing a fuse 23 as referenced in the post
here and as if by magic I am back in action. The green dragon drives again just like new.
Hope this helps someone.