The rectifier behaves like a direct short when wired backwards, and it is not fused. (Honda technicians are supposed to know better than wire the bike backwards and if they don't learn this quickly, they find jobs in other trades.) Anyway, this makes all the wires between the rectifier and the battery heat up and melt their insulation. Any wires routed near them in the wire harness also have their insulation melted. Find the rectifier and replace any wire that doesn't have proper insulation. Follow these melted wires into the harness and keep unwrapping the harness until you stop finding melted wiring to replace.
The rectifier may be damaged, too, so measure it (see the FAQ).
Good luck.