You won't get an accurate reading if the battery isn't fully charged and installed in the ATV when you check the voltage. The voltage regulator has to sense the battery voltage to be able to properly regulate the voltage. However, without a battery installed, the voltage will usually read higher than normal. To be sure, I would get a good, fully charged battery and put in it and check the voltage at the battery with the engine running. If it's still low, you probably have a bad regulator/rectifier providing there is no wiring problems. Also, make sure the connection to the regulator/rectifier is clean and tight.
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