To fix this I would first take a deep breath, get me some beer and pop tarts, and then sit down with a wiring diagram for my bike and a notebook to keep track of my progress. It might be helpful to also get some masking tape and a sharpie so you can label the wires as you sort through them. The most likely problem will be a positive wire hitting ground. This might be a short from a damaged wire, an exposed connection, an incorrectly connected connection, a faulty component, or some combination of these.
Ask your self some questions: Does the fuse instantly blow? When does it happen? Can you do anything w/o the fuse blowing? Does it blow in all key positions? If I can turn off the headlight, does it still blow? These are all valuable clues to track down the short. If anything works before the fuse blows I would make note of this -- those things are less likely to be the problem.
1) The way you described the problem as intermittent and seemingly random makes me lean toward a loose connection, or an exposed positive wire/connection that is contacting ground. I would start by attacking those bullet connectors with a multimeter (or test light), and I would figure out which ones are positive, which ones are ground, and which ones are something else. I would insulate all of them, starting with the positive ones. I would pay close attention to the wires, and carefully look for any place where an exposed wire could touch anything.
2) If that did not solve the problem, then I would do my best to try and isolate what is blowing the fuse. Start by trying to figure out what some group of wires does, then disconnect them. See if you can get down to the bare bones, and then work your way through the components: ignition system, charging system, head light, tail light, blinkers, horn... until I was done.
3) I remember an old bike I once had that had a weird misfire that was driving me nuts. I had the bike race tuned, then it started just running like crap. I eventually figured out that the problem was a perfectly good looking kill switch which had a broken contact inside it. The thing would jiggle internally with certain RPM's vibrations, micro-breaking the contacts, and "killing" the motor thousands of times a minute. That was my mysterious misfire. This story always reminds me that sometimes the most obvious thing might be the problem.
a PO's wacked-up custom wiring can look and feel like a real electrical system nightmare, but keep your cool, and keep reminding yourself that the bike only has a few components to the whole system. When it all boils down to it, it is not all that hard to find any electrical problem on a bike. I will not be surprised if you have this all sorted out by the end of the weekend. Good luck.
peace and grease,
-fang
