I've had the alternator connector block melt on one of my Hondas. The issue was corrosion that built up in the connector itself. This raises resistance and results in temperatures hot enough to do damage.
The fix:
1. If you have not yet had this problem, disconnect the connector block, spray it with contact cleaner, hook and unhook the connectors a couple of time to burnish the leads, and then coat with a light coating of dialectric grease to prevent future occurence. I now do the dialectric grease thing on every connector on every new bike I get as soon as I bring the new machine home.
2. If you have already melted the connector, buy a new male/female connector block with sufficient terminals at Radio Shack, cut the wiring back to where it is not damaged, install the new connectors, and protect with dialectric grease as outlined above. You may need to reroute things a bit to get enough wire length when you cut off the old connector blocks.
