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Special Update!
I previously reported that the F circuit from the enabled regulator (5v to L terminal) would read ZERO volts until the engine was started and the alternator was turning. This was in error. In actuality, any time the alternator is enabled (power to L terminal) the regulator will begin pulsing the rotor. With the engine not running, this pulse will have a duty cycle of approximately 30%. Although this opens up another diagnostic angle for diagnosing a charging system problem (shown below), external faults on the F circuit will not prevent the alternator from charging (see part 4)

Special thanks to John Thornton for pointing out my error.

I left you all with this question:

Do we now know enough to determine what was wrong the vehicle Miles was working on?

I believe we do. Let's first start with the assumption that we already know that the alternator is not charging. We also know that the large output wire is connected to the battery. Miles mentioned this:

I also have to mention that the alternator light does not come on with the KOEO or while the engine is running but if you turn the key on, off and back on you will see the alternator light flash momentarily.

For the alternator (battery) light to be on, voltage on the L terminal must be low. With the key ON and engine OFF, the 5v supplied by the PCM to the L terminal should be pulled low by the alternator since it is not charging. If the alternator lamp does not come on during KOEO, then the connection to the alternator for the L circuit is either defective or the alternator is not pulling down the circuit as it should.

Miles made the following measurements for us

With the connector off the "L" terminal measured 5 volts and the "F" terminal measured 0 volts with the engine off or running.

I would be ready at this point to replace the alternator, but lets dig further...

Take another look at his KOEO readings. With the L circuit sitting at 3.65v, the PCM does not see a low enough voltage to inform the IPC to illuminate the alternator lamp. A good alternator should not do this. If the alternator is not charging, it should pull the voltage down further.

Miles did mention that the lamp flashed just for a moment upon key up. I believe he is correct in assuming that the downward spike (in yellow) is what caused the PCM to illuminate the lamp just for a moment.

Another problem here is that the F circuit should be toggling between 0 and 10 volts (about 30% duty cycle). Instead it is sitting at 3.58v

Now lets take a look at the available scan data. First however, lets look at normal KOEO waveforms for this vehicle

And now the accompanying scan data.

The L terminal is "Inactive" meaning the PCM is applying the 5v. The F circuit has a 27 % duty cycle which is normal. How does this help us? We know from the F circuit duty cycle that the PCM has not only commanded its circuits to apply 5 volts to the L terminal, but that it is actually getting there.

What would happen if we unplugged the regulator connector? Lets take a look....

Here we see that the PCM believes it is applying 5 volts to the L terminal but that the feedback from the alternator (F circuit) is (assuming a good regulator) telling us otherwise.

Now lets plug the regulator connector back in and start this baby up.

Looking good!

Consider something now....
If we had a few diodes that were burnt out, would this cause our L circuit voltage to drop and illuminate the alternator lamp? Could we use the Generator (F terminal) duty cycle information to help determine if we had defective diodes or a bad stator? What would happen if the F circuit became grounded while the engine was running?

Stay tuned for part 4!