It seems to me that (1) you need to strip out the old wire and either (2) get a harness from Mike or whoever if you plan to keep the bike more or less stock or (3) run you own wires if you plan to chop or bob it. You need a few rolls of 14 ga in orange, brown, green, red, yellow and black.
I ran my own, soldered each connection, either shrink wrapped or Plast-Dipped the connections, bundled everything in flexible slit plastic conduit and zip tied it up neat. Used a Dremel wire brush to clean out the light sockets and dielectric grease where needed. Got a blade fuse block from Advance Auto Parts.
Its really no big deal, with a bobber or chopper you just need a few wires. A lot of the electrical paraophenalia on the stocker can be discarded (brake lining warning, headlight out warning, etc.) The only things I kept were the flasher, the starter relay (next to the fuse box in the pic) and the finned regulator that came with the SparkX alternator (mounted on the fender under the seat in second pic). ONce you throw away that extra junk, it will become clear how simple it is. THere are some good simplified elec diagrams here, hit the tech sections here and on 650Motorcycles.com for more advice and drawings. Go for it!
Nice wiring setup. Question: what did you use as the base of your wiring/fuse/starter relay? The mesh stuff? Did you just cut it to shape and bolt it in?
Thanks