Check the Green ground wire between the rectifier, up through the harness to where it attaches to the frame at the coil mount.
Even a momentary reverse battery connection can take out those wires as well as the red ones.
In some rare cases where the battery runs too low on fluid, the charging system over currents and ruins the wiring.
Check rectifier six diodes, as it can take these out too.
You can check regulator function. But not much the stock one can do to make wires burn out unless stabbed by an axe.
Cheers,