high voltage stock 6.1 alternator
From a glimpse at the wiring diagrams, i suspect that the PCM (powertrain control module) sends a PWM signal to the alt to control field excitation.
The old VR does something similar, it contains a transistor placed in series with the field winding in the alt, closing the circuit it to ground rapidly, much like a PWM signal.
It's setup at the factory, for a very old alternator and i think that's the problem.
What happens if you remove one of the wires from the field excitation winding?
Does the voltage drop to battery voltage?