The factory Miata wiring harness (at least for the MSM) is really four pieces:
- Engine harness
- Passes through the firewall near the passenger side of the engine bay
- This is the only harness to directly connect to the ECU, though some wires do originate on other harnesses
- Connects into the main harness and the dash harness, roughly behind the radio
- Dash harness
- Primarly for HVAC controls, radio, and similar controls
- Connects to the main harness and the engine harness
- Main harness
- Extends up both sides of the engine bay, to include headlights, sidemarkers, engine & A/C fan, ABS
- Includes the main interior wiring, such as instrument cluster, door sensors, etc.
- Connects to all other harnesses
- Trunk harness
- Includes fuel pump, tail lights, trunk sensors, etc.
- Connects to the main harness behing the driver's seat, against the right rear tire well
From all of those harnesses, I removed all of the outright obvious stuff: HVAC, power windows, power locks, ABS, radio, speakers, door sensors, ... For now I left the engine harness completely untouched to limit the complexity of troubleshooting.
One interesting find was that the factory MSM engine fan has a 3-speed motor, with three separate relays. With me installing an aftermarket fan, I eliminated "medium" and "high" fan speed relays, and only retained the "low" speed relay (RED/YEL signal wire from the ECU, YEL power feed to the fan motor).
Take your time, be methodical, check the wiring schematics repeatedly before cutting out any of the wires. Also, for your sanity, I advise you label every connector with painter's tape.
What's pictured is the "after", with the box of wiring representing what all was trimmed off.