One popular and effective technique for laying out small-to-medium harnesses is through the use of a physical template. Make one sample harness with bundles lashed together only at critical points, and test it for accuracy. Now build a platform a little larger than the harness and lay the "go-by" harness on top of it. At each breakout, drive nails or screw down short battens to indicate the breakout location and direction, folding the "go-by" breakout around the nails/battens. Also at each breakout, tape down a color-coded diagram showing the colors of the wires involved in that breakout.
At each connector location, tape a drawing of the connector with color-coded wires going to their correct locations within the connector.
When you're finished, you should have no loose ends, and every breakout and connector will have a drawing from which to make duplicates. Remove the "go-by" harness and staple cardboard boxes at each termination point - you'll fill those boxes with the appropriate connectors for each termination.
Now you can set up your spools at one end of the template and very quickly make another harness that fits the same template, with all the correct wire lengths, and with the correct connectors already laid out in their respective locations.