Did you download the wire diagram? I would consider looking into the headlight bucket, and ensure the connections don't look toast, or cross connected. Verify all the grounds are fine. and continue following the wire diagram. wire diagram should be on the stickys on top of the page, on about the 4 page. (if I remember right)
http://www.xs400.com/threads/chargi...tor-or-dead-charging-system.7567/#post-155915
http://www.xs400.com/threads/chargi...tor-or-dead-charging-system.7567/#post-155915