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The ecu doesn't have anything to do with the start circuit other than the orange wire that tells it to use the cranking map.
Also, was this originally an auto shell or manual shell? If it was originally manual trans, you need to bypass the clutch interlock switch not the neutral safety switch. It's a large relay with 2 connectors in the front passenger corner of the engine bay by the neck for the washer bottle.
If that's what you meant and it has already been done, I would start at the start position contact on the ignition switch and chase the signal along the chassis harness until you know longer see voltage. Sometimes these seemingly simple circuits are tedious as he'll to troubleshoot as you are definitely finding out after 18 months.
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