Welcome to the Team Brad!
We can talk about how the factory did things, as that is documented in wiring diagrams and everybody is fairly familiar with how the factory ran their wiring. What no one can help you with (at least not over the internet) is what some one might have done to your car in the past. This is because we can not see it and haven't a clue what someone might have done to your car.
I can suggest some simple tools to diagnose electrical problems (since you can not see electricity). The first is a multimeter. You will need one that is digital and has auto range features and includes Volts (AC-DC) and Ohms and continuity at a minimum. You can find many models to choose from at RadioShack.
While you are there buy a 25 foot spool of 12 gauge wire and two small alligator clips and one big one (you can use the small clip to make an electrical connection with the big one). This is used to provide either a known ground path or power as needed for debugging. A simple steel needle sharp probe with a light in the handle is also useful as you can stick the steel probe into connections that have been terminated to test the circuit without destructive insulation removal to get to the actual wire.
You will need a full size wiring diagram (the engineers drew these on D size paper that measured 24 inches by 36 inches), so if it appears a little small and hard to read on an 8-1/2 inch by 11 inch paper you know why. You can buy full size color copies of these fold out sheets that were originally used by line mechanics to repair cars, but you have to look as everyone sells a smaller copy normally.
You will also need a wire termination kit with a good selection of crimp on terminals and splices, a soldering gun to make the crimp on connections better conductors of electricity and some rosin core solder in various small diameters. Wouldn't hurt to buy some liquid electrical tape and shrink wrap with access to your wife's hair drier or a small heat gun.
Or you can just buy all new wiring from American Wire and install that instead.