Quick question regarding the wires: are they 3 yellow wires? If so, this is a common problem with older Honda charging systems. The 3 yellow wires are the coils coming off the alternator going to the rectifier and regulator. There is a connector between the two which will degrade with time, increase resistance, and eventually fail. The connector can be bypassed by soldering the wires together, with some shrink wrap to protect them from shorting or the elements.
If not, please disregard. I agree: burnt wires are a bad thing, usually a sign of excess resistance.
Luke M
Used to have a 1979 CB750L, sold it as a parts bike, now riding a slightly modified 1984 VT700C. Network/Field Engineer. Central OH, USA, Earth, Sol System, Milky Way Galaxy, Universe.