Wiring Clean-up/Simplification

What I ended up doing was unpinning the wires from the connectors. You'll have to "open up" the connectors. Usually there is some sort of wire keeper on the back of the connector ( harness side ) and you'll need some small pick to push down / in on whatever pin keeps the actual connector in the plug. Although it's tedious, it's not hard.
You could use the FSM to identify the wires, but it also should be fairly easy to follow an open ended wire back to the connector, and "unpin" it.