I thought perhaps you had a different version of the XR400. In the US XR400's did not come with batteries either, sounds like same version you have. I believe Honda sell "Street Legal" XR400's in some countries. These would be substantially different. Honda discontinued the XR400 in the USA in about 2002 or so. They make various versions in Brazil using similar motor.
My '98 XR400 had a Baja Designs kit on it. It did use a small Ni-Cad battery pack to allow lights, horn and signals to work with motor off. This is a legal requirement in USA. Excellent system, 100% reliable.
So you're running 100% off the Stator. Nearly sure to be bad Reg-Rectifier.
But have someone qualified check it out to make sure. Takes about 5 minutes to do the checks using a VOM. (volt-Ohm meter)
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