I also added a parallel 14GA wire from the output post on the alternator directly to the Ammeter. I bypassed the Ammeter by connecting all wires to one terminal. I ran a ground direct from battery (-) to the VR Ground plane (chassis). I replaced all the terminals at VR, Alt, and Ballast. I also added a missing ground from the engine to the master cylinder bolt (cleaned), Installed a rebuilt alternator and a new Interstate Battery (fully charged) and tried it again.
Output at Alternator to Bat (-) @Idle: -0.5VDC (DMM (+) on Battery, (-) on Alternator)
Output at Alternator to Bat (-) @2000RPM: -2.3VDC (DMM (+) on Battery, (-) on Alternator)
strongly suggests the battery is taking a lot of current.
If the electric fanpowered from the battery, move the connection to the alternator. That will reduce the load on the wiring between the battery and the alternator output stud. That wiring clearly has too much resistance for the load going through it.