Flickering head lights, what am I missing

The FIRST thing I'd do is upgrade that 18 ga wire in the field/ regulator circuit. One thing you need to realize is that the VR/ field circuit PULSATES and one reason it is not normally noticeable is that the inductance of the alternator field itself sort of averages that out. However, with a long run of too-small wire, you can set up interesting feedback/ oscillations type of deal. The VR power (IGN) terminal MUST "see" "same as battery" to regulate correctly that IS the sensing terminal.

In fact, I see no reason to wire it the way that you did. If you use the small terminals of a 4 terminal (double pole) disconnect to control a relay in conjunction with an ignition switch, you can then pull power for ignition/ field / regulator off the large main feed "up front" and eliminate voltage drop problems