I just rewired my GS500 (a couple of times, since the first was a major learning experience) and I can tell you, it's likely a bigger project than you're expecting. For starters, do you mind if I ask why you're doing it? And what exactly are you planning to do? It sounds like you want to replace the current harness with a new, homemade one. If that's the case, here are some things to consider.
Will you reuse the same connectors? If so, how will you connect them to the wires? I would not recommend using butt splices, as they serve as just another point of failure later down the road. Only use these when completely necessary, but they are good to have around. You should try to get quick disconnect terminals, like these (I call them male and female paddles, since I've yet to find a succinct name for them). The trouble is, in order to fit in the connector blocks, they need a barb on the back of the female to hold it in place, and I couldn't find any such terminals. I ended up replacing all of them with [weatherpack](www.weatherpack.com) connectors, but that was likely overkill.
What wire will you use? I was a cheapskate, and I chose not to buy the various colored wire that the bike used. Now it's pretty much all black and red wire. This turns out to be really difficult. If you can avoid it, don't do this.
And do you have your service manual? If not, get one. The wiring diagrams are invaluable. I absolutely could not have done this without the manual. It's the greatest investment you'll make for your bike.
Make sure you understand how every electrical subsystem works before you really delve into it, and it's really not that bad. And the knowledge on the other side is great to have. You'll know every square inch of your electrical system.
Oh, and a couple of things I found helpful. I put an ignition-switched power and a ground post at the rear of the bike. Just a bolt and nut through a hole in the fender. With ring terminals and another nut to hold them all in place, it serves as a great way to power and ground anything that needs to only be on when the key is turned. And it's easy to add things to it later.
In general, cut all of your wires long. Label them accurately—I used painter's tape—and cut them to length as you're adding the connector. Saves much confusion.
Good luck.