We try and make every harness as close to stock as possible.
The only difference is with the wire coloring. Stock wires will have a colored band going down the wires length identifying the secondary Color Code. For Example a Red wire with a Black Stripe.
Because of the tons of variations in colors we have found a solution by running the primary wire color and then attaching colored heat shrink banding every so often along the wire to identify banding. This has worked really well and allows you to still follow schematics wiring colors.