REPAIRED and RESOLVED! Here is the final outcome and procedure:
I disconnected the PCM connector (after removing the battery and the battery box in order to get full access to the connector), located the coil lines on the connector, and then checked them for continuity to the coils. All 4 of them checked out perfectly (effectively 0 ohms). So I'm starting to think, "Hmm, I may have a bad PCM."
At this point, I also checked the A/C accumulator as had been suggested. It turns out on my truck, the accumulator is mounted fairly low and only a battery cable (running down to the starter) runs anywhere close to it. So that was not the problem.
Nonetheless, I carefully put it all back together and re-check the signals with my LED test light. Voila', all 4 signals are now there (as mentioned early on, the ground pulse signal to coil B signal had been missing previously).
I start it up - it's better but still missing a bit (not nearly as badly though). I swap the 2 coil packs, better still, but after a good bit of running time it eventually gives code P0354, coil D (it had been P0352, coil B). Obviously, the miss followed the coil pack. Again, I check the resistance of all 4 coils, paying special attention to the 2nd coil of that particular coil pack; and again the primaries check (~0.5 ohms on each coil), and the secondaries check (~14K on each coil). All 4 primary and secondary coils measure with perfect resistance!
I finally decide to replace the coil pack anyway, which I did this afternoon. And the engine is now purring beautifully once again.
Conclusion: I had not been getting a pulse on coil B from the PCM earlier, which was solved after I messed with the connector. I wonder if disconnecting the PCM, cleaning the contacts (which I did with electronics cleaner, even though the contacts looked perfectly good), and reconnecting acted to re-establish the connection of that coil pulse. It also just so happens that the pins for all 4 coil signals are on the last column of pins of the connector, which puts them at the extreme bottom of the connector once it's plugged in (the connector plugs in vertically). Then I also noticed that the very hefty wiring harness on the connector tends to torque against the connector, putting a force on it that tends to pull the connector upward (thereby tending to unplug the connector starting at the bottom, where the coil pins are). And yes, there's a hefty bolt holding the PCM connector in, but the connector is so large that the ends can clearly still move a bit when under pressure. So the question would be, if the coil had been getting a weak (and eventually no) ground signal from the PCM, could that end up weakening the coil itself until it eventually failed? And weirder still, cause the coil to fail in such a way that it ohmed out right on spec?
I don't know, it's all conjecture at this point. But clearly - it took both of working with the PCM connector and then replacing the coil pack to completely solve the problem. And I did not end up having to replace the PCM! But it sure took some time, effort, and thinking to track this one down.