Voltage Regulator

The first place to start;

Something on the VR not wired correctly? Double check your wires.

Do, the wiring wasn’t changed at all. I removed the entire black connector and plugged it into the new voltage regulator. I thought maybe the battery terminal connector may have come loose inside the black connector, but the pilot said the charging system was working fine in flight. If the yellow wire connections aren’t good will the voltage regulator burn up? Or if the battery terminal inside the black connector that goes to the voltage regulator is not connected will the VR burn up? 

If the wires are not pushed on all the way and are a lose you can get arcing, but I haven't seen one smoke. Maybe another wire leading up to the plug is grounding out?

A number of folks I know have had VR failures with indications of hi heat on some of the connections in the big plug. When checked individually they were not tight. Before you click the individual connections into the big plug housing, I believe it is imperative that you check the tightness of each one on the mating tab, and pinch down the spade terminal if any looseness is detected. Some folks are discarding the big plug housing and just using the individual connectors-much easier to detect and troubleshoot any problems.