Thanks for the advice. I have verified all connections and bypassed the harness connector. Here is the latest.
With the Headlight and Taillight fuses removed, the charging system works correctly. Engine at 2500 RPM, battery-voltage equals 13.5. Engine at 5000 RPM, battery voltage equals 14.6.
Whenever one of the fuses is put back in, the charging system does not work. Battery-voltage is now 12.3 - 12.8 depending on RPM.
Last night during extensive troubleshooting, I was able to the battery to start charging for a short period of time with the fuses installed. Now I am hearing chattering from the Junction Box when the two fuses are removed and the charging system is working. Once again though, as soon as one or both fuses is installed, the chattering stops and the charging system stops working.
I am thinking maybe a relay inside the Junction Box is not latching or unlatching and this is the problem.