Thanks for the info on the Electra, Mr. Adrian.
I'm more of a student of this technology than a professor, but here is a link to what I would consider pertinent and interesting information on this type of 3 phase charging circuit, including a sample waveform and a typical schematic of the Rect/Reg.
https://electronics.stackexchange.com/questions/235195/3-phase-permanent-magnet-alternator-with-regulator-rectifier-scr-output-wavefoRE doesn't give us details of the circuit they use for voltage regulation, but we know that the alternator is the permanent magnet rotor type. There's no field coil, so output of the alternator is proportional to rotating speed ( and magnet strength of course). The rectifier converts AC output to DC pulses. If the regulator follows the simple design shown on the linked site, it monitors voltage of each of the 3 phases, and shunts the output to ground whenever voltage exceeds the reference voltage.
I'm thinking that this regulation process could be messed up if the voltage reference was wrong, and I think that this could be caused by high resistance wiring or high resistance connections at several points. I'd take a close look at the connections of the Battery - to ground, the condition of the Battery + terminal, and the wiring and connection of the Rect/Reg to the harness. I'd measure resistance of the various wires. These should all be fractions of an ohm. Copper wire can oxidize inside its insulation and become a crude resistor. Wiring that is close to where the battery outgasses is especially vulnerable. I'd disconnect and clean all connections in the charging system. Connections to the steel frame and within connectors can develop an superficial oxide layer that can be quite high resistance. Wiring and connections thus degraded will show continuity, and it will conduct, but it changes the system voltages at various points, and wastes power in the resistance.
Good Luck!