I didn't know about the different ECU's that were in your car. So now I am going back to the wires,... I am convinced that you should splice a wire right at the ECU connector (that pink one) and run it all the way to the neutral switch itself. None of the junctions and connections matter,... just bypass them all with a double lead speaker type wire with one going to the pink wire and one to ground (like under a bolt on the kick plate). I'm pretty sure the switch doesn't ground to the transmission when it's closed so the polarity (pink or ground wire) doesn't matter at the neutral switch. You can test for ground to the transmission by disconnecting the switch and testing for continuity between each wire (terminal on the switch lead) and the transmission (engine ground) for both in and out of gear. There should be no continuity between either terminal and ground, in or out of gear. If there is continuity between one of the leads and ground that wire needs to be the ground wire.
It sounds like you didn't actually replace the entire length of wire from the ECU to the switch and testing the wires for connectivity may not work if the wire is broken inside of itself and making occasional contact, like when you test it with the engine off,... it could be the vibration of a running and moving car that makes and breaks the contact in a broken wire.
Replacing the wire should be really easy,... just ignore the junctions and colors and rewire the entire length. I'm 98% sure that doing that would be equivalent to replacing the entire harness. You've just got to replace the entire length of suspect wire.
You simply don't have to trace the wires,... the schematic shows clearly that the electrical path goes directly from the pink wire to the switch and back to ground and doesn't go to or connect with any other circuit. I'm positive you should try this before you replace the entire ECU harness,... with all the work you've done so far you could have it done in half an hour,... if that doesn't work then spend the big bucks and hours replacing the harness.
Two dollars worth of wire and half hour of your time and I'm almost positive it will fix your problem.
The wiring schematic is in the P5-Wire section of the service manual on page 24,... it shows the pink wire going straight from the ECU to the switch. The black wire (ground) goes to numbers 3 and 4 with a circle around them. I'm thinking that is where and how it plugs into different junctions and goes through color changes but it eventually goes directly to ground.
You're not really wrecking anything by cutting and splicing the wires if you end up replacing the harness anyway.
I am in fact so sure that this will work that I am willing to cut and splice my wires 2" from the ECU and 2" from the switch to prove it. I won't even look at the other junctions and wire colors, only the pink/green and ground. Just let me know.
I will at least go out to my car tomorrow and test the continuity of the switch to see if it grounds to the bell housing or if it only grounds to other lead wire. If it doesn't ground to the bell housing (as I'm suspecting) then the polarity doesn't matter and the pink/green wire can go to any lead and the other one can ground anywhere,... I'm thinking to the engine block somewhere. I've got an oil change to do anyway so I'll do that tomorrow.