All of the dash indicators are "hot", they dont turn on by being grounded negatively like the rest of the electrical system, they turn on by being grounded positively. My guess is that when the system shorted if probably fried something there, too. I'd pull the front plastic and dashpanel off, and start tracing back from the indicator lamps, I believe they all have a brown wire in common. Easiest thing, start with a test light, and trace them back. Is there anything installed on the bike that would've drawn excess power through the wiring harness, like additional lighting without using a relay? Good luck man.
Oh, do you know where the short is/ was yet, have you tried splicing in a jumper wire past the short? I had a short that occurred on my 04, at first I though it was the rectifier, I saw a wiff of smoke coming out of the plastic panel beside it. Once I pulled the rear plastic off, and started wiggling the wiring harness along the frame, I saw it short and arc out where the harness started to go up the frame to the fuel tank, just past the rectifier. It had rubbed itself through the protective tape and shorted against the frame. Taped up the individual wires, taped up the harness, then wrapped it all with some wire loom like the factory should have. Hope everything works out for you!
