I had to replace the loom on my FJ1100 after it melted - was corrosion in the connectors which raised the resistance and therefore drew more current and overheated.
Bought a new loom from Yamaha and fitted it, so my first suggestion is try the bike manufacturer - if you can afford it! Worth a call though, you never know.
If you have a multi-meter (and if not why not?  ) then you can check all the wires out for shorts to the frame (battery negative) or to each other. Best to unplug all the connectors you can so you don't get parallel paths through light bulbs etc.
If it's just one section which has melted through, you could always make up a short replacement loom for the bad secion, and either solder it in, or crimp bullet connectors / suitable plugs & sockets onto the ends of the wires and install it that way - might be easier than stripping the whole loom off the bike.
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