Hey Mark, that sucks... I would guess that it probably isn't the #3 relay. A few things wouldn't work like the fuel gauge, temp gauge, taillights, but the bike would still run and could still be started. I would take a look at either the battery or the dogbone fuse like was mentioned. If you can't find a replacement fuse, and you have the stock alternator, you could always substitute a 50A one like
THIS ONE I have a compufire and didn't like using dogbone fuses so I used a 70A fuse like that one on mine. You just have to cut a hole in the fuse cover. And as far as the battery, I had a similar incident after installing my compufire. My bike ran fine the first day after putting it in. However the next day, it died and the bike went completely dead. No lights, no starter, nothing. With a voltmeter attached and the bike off, it had over 12V of power but as soon as I turned the ignition on, it went dead. It turns out that there was at least one bad cell in the battery. It would still test as normal at the store and I had to go to 2 stores before I could convince them to replace the battery under warranty. But once the new battery was installed, the bike fired right up and ran fine.
I can't remember, do you have a voltage meter on the bike and if so, did you notice anything unusual prior to it dying out?