Heh.. i just got done completely redoing my electrical harness. The wires are color coded.. so it shouldn't be too hard to figure out where stuff goes. You can click
here to go to Yamaha's parts catalog and check the wiring harness on there... although, i doubt you'll need to.
Just be sure your grounds are on correctly... my problem was that they weren't grounded right and completely killed my spark for a good 3 months. =/