Hmmnn, the spade connectors on the terminals are a useful notion for these occasions, and as ChrisG says there's a great deal to be said for having a fuse one each line.
I use spade fuses too, 20A (17A if you're a purist).
Your bike has some sort of dead short which you'll find as you replace the melted wires.
E-mail the machine to me and I'll go thorugh the wiring if that helps.
If you're lucky Brown/Blue is Live and Red (as you've already said is Earth.
The electronic ignition will almost certainly have required a reversal of the earth polarity thingy.
I'll be glad to look it all up properly for you if you get stuck.