Have you found the wiring diagram for your truck in the information section yet? Print this document nice and big, and field-verify the wire runs you're confused by:
http://www.luvtruck.com/PDF/Series9&10.pdfDon't trust any wire colors, generally speaking. There are a few places where a wire is spliced into a harness halfway through the run, and there's no guarantee that the colors match. That is how these trucks come from the factory, by the way. And who knows what else has been done in the mean time.
I used a few different colored highlighters to keep things organized.
It looks chaotic, and the lines are too close together, but it's a smart diagram - laid out like a truck from above, making it relatively easy to figure things out.