How can I fix my Kohler Command 16 hp lawnmower engine wiring?

I have an Kohler Command 16 hp ohv engine on a 42" Craftsman riding mower that I purchased new in 1999. Two wires coming from the regulator/rectifier (credit card shaped piece with three wire connectors screwed onto the outside of the flywheel housing) became so hot that they burnt through the plastic connector/harness and burned out the wire. I reconnected the wires and it started right up. After about thirty minutes, however, I felt the wires and they were VERY hot. What would cause this and how can I fix it? Any help would be greatly appreciated. This is a Kohler Command, OHV 16 hp engine family: SKH426U1G2RB, model #: CV16S, Spec. #: 43514, Displ. 426 cc.