If it was my car, I'd take each wire, identify it by color and location using the diagram, number it with a wire label according to the diagram, and locate the other end and label that. Once you have done that. connect both ends where they are supposed to go and move to the next wire. Tedious, but it should both get the wires back to where they belong, and show up any weird modifications. If you get stuck on a modified wire, move on. Eventually 99% of it will be connected correctly, and you can then resolve the odd parts.