Another thing to be careful about is similar to physician's credo, "Do no harm". In diagnostics, it means passive measurements ONLY with no changes to system. Measure voltages, resistance and perhaps current only, but do not apply power and do not make any changes to wiring or components. This lets you identify exactly problem area through numbers. THEN when problem has been positively identified, make that ONE change only.

What typically happens is desperate shotgunning of parts, which introduces additional variables and possible errors into system with low-quality non-OEM parts and you end up running around in circles. Since you never positively identified broken wire in original harness, how do you know replacement one doesn't have broken wires as well? It may even have MORE broken wires than original. Only way to tell is...?

So again, don't make changes to system, only passive, non-interference, non-destructive measurements and let the numbers speak to you.

 

Didn't see any mention of this:

neutral switch - does dash green light turn ON when gearbox is in neutral?
clutch switch - is part of either/or/yes/no logic of safety-interloc circuit

These along with kickstand are directly connected to ECU and it will kill engine by cutting off sparks and fuel-pump if it detect unsafe condition. It's not enough to verify these devices are operational. The wires in between them and ECU must be OK in order for signal to arrive.

You are not Superman and cannot see electrons flowing inside wires. Nor can you see broken wires inside insulation. Use multimeter to verify these wires are continuous from switches to ECU.