here are some things that worked for me:
pin your wiring diagram on a piece of foamcore or plywood so you can reference it easily and pin notes beside it.
do a good search on wiring problems, and cut and paste what's relevant to you into a word document and print that out. there are four or five guys here on the forum that really know the electrics on these bikes.
look at the headlight bucket and try and visualize the wiring in groups - you've got a bundle coming in from the main harness, another from the left control, another from the right, the gauge light wires, etc. it looks like a mess but there is a design there.
take off the tank and side covers and trace the wires back and learn the whole harness. you'll save time and stress that way. future problems will be easier to deal with.
clean and lube all the connectors while you're at it, the bike will run better.