Update on this post: It was a diode in the crappy new alternator. Don't buy Wilson products.

Went to a reputable shop in my town that specializes in rebuilding alternators, among other things, and as soon as they saw the Wilson box, they immediately told me that was garbage. A bad diode was causing the rhythmic dimming of the headlights despite showing to be putting out 14 volts. I cleaned up my grounds, cleaned all contact points, new cable assembly and tried playing around by plugging and unplugging the Variable Voltage Control Sensor on the negative cable and nothing changed. I swapped in an old OE Nissan alternator I had laying around and it started performing perfectly. I'm going to have rebuilder give it a refresh here soon.

Thanks for actually following up on your post!

Yeah, Wilson is junk. I won't even install it if a customer asks!