Update on troubleshooting. I decided to wring out the wires from the alternator. The charging wiring diagram shows a yellow wire that has a diode somewhere, routes to the ignition coil, fuse, and finally the ignition switch. I noticed the engine control diagram also shows the continuation of that wire from the charging system, and feeds back to the MPFI/ECU. To confirm the MPFI input, I connected my ohmmeter from the alternator yellow to the MPFI yellow, and had continuity. I'm going to disconnect it at the alternator connector.
Placed two jumpers to the alternator for the white and black wires. The car seems to start, run, and charge the battery!!! Don’t know why, but I’ll take it.