Finally
I think...
It only took 8 hours of disassembly, google search, head scratching, crying, bargaining with God, and luck. Mostly luck. It was a somewhat anticlimactic solution; a loose connection. Ask me which one and I'll tell you I have no idea. All the parts in the charging system tested good individually, so after cleaning the connectors and re-assembling the parts the system performed within normal limits. We'll see if it lasts.
Usefull resources:
Charging Troubleshooting Flowchart Print this out, it was a lifesaver
My Mower Parts Online Kawasaki manual for the fj400d engine
ElectroSport Industries "How a Motorcycle Charging System Works"
