Hi Chopped,
If it were my bike I'd wire in a few fuses now, not necessarily permanent, but I use them for testing. I do like fuses in major circutis for later.
In buses and trains we have thousands of wires and if you have an intermitant short, or one that only shows up on a bump they can be hard to find.
A trip to Radio Shack and a few fuse holders for testing can be quite handy.
You isolate each circuit and install an idividual fuse, if it burns out you know where that one is. I found a worn wire on my horn circuit under the faux tank on one of my Goldwings this way last summer. It was quite irritating as three items were on the circuit and it would only blow a fuse once a month.
Once you know what circuit an intermittant short is on you can concentrate your search there. The less wired together the better.