Flickering head lights, what am I missing

There's the most likely cause - assuming its only at slow idle speed.
Voltage is rising and falling because the alternator can't supply that much power at 14ish Volts.
So voltage drops down until it equals battery voltage.

Bring the rpms up, or increase the load and it will stabilize.
Don't do that second test for a long time.

this is 90 amp alternator, wiring has been upgraded, running all the new accessories through relays,
the flickering is at idle and at higher RPMs, obviously the fuel pump and MDS draw are always present when the motor is running, having the electric radiator fan running or not has no impact on the flickering.