I had the same mess under the fender, I purchased my bike used also. 
Look what I have to deal with now, under the seat (click on the picture to expand):
It looks like a rollacoaster in there, hehe. I already removed all wiring of my bike, all that is left are the metal parts.
The wires are pretty damaged, I need to order the full harness... It costs "only" $400.00.
2003 Night Demon - pics will come soon... working on mods.