In the interest of full disclosure and for fun I thought I would update this string.

Last week, as my wife was driving through our neighborhood on the way home from the store our 4Runner just stopped working. She said it sputtered and lurched like it was out of gas, the dash lights all came on, and it coasted to a stop...We had it towed to our local service station (not the dealership.) They were not able to connect to the PCM via the OBDII link, no communication, and proceeded to manually test the different systems to see what might be the problem. Eventually they conceded that the PCM itself must be bad.

They found a used one at a local junk yard, installed it and the truck is back up and running. Only time will tell but, so far, no shifting problems.

I had previously thought the PCM might be bad, even debated the pros and cons of replacing it with my dad, but had an impression that was less likely than it turned out to be. My mistake cost me about $500 in diagnostic testing (a used PCM is relatively inexpensive and dead-simple to replace.)

Thanks to everyone who threw in their $.02 on this thread. I really appreciate you taking the time.