I had a Honda ATV in the shop today that had a charging problem. It took a while, but I eventually tracked it down to a corroded wire going to the voltage regulator.
ATVs around here operate in a salt water environment and it leads to a lot of corrosion problems. The voltage regulator on this machine is mounted under the rear fender near the tire. It routinely gets sprayed with water and mud in this location. It appears that the insulation on the wire was cracked where the wire bent sharply going into the plug. The cracked insulation let the salt water get in and corrode the wire.
It was a simple job to fix. I trimmed out the bad section of wire and soldered in a new piece. When finished I made sure to seal it up well. I like to wrap connections like this with electrical tape and coat them with "Liquid Electric Tape." In this case I was out of the Liquid Tape so I used tape a coating of RTV silicone. Adhesive shrink tubing also works well, but you must have the type with adhesive inside. The cheaper kind without the adhesive does not work as well.