While I havent done a proper engine conversion, logic dictates that as long as you cover the appropriate inputs/outputs that are separate to the engine loom then it should run - ie the bits you mention and not the injectors, ignition ect. Though what engine are you looking to fit and into what car?
Items to also consider:
- Speedo - normally comes from the cluster to the ECU, not normally important for a manual but essential for an auto
- Some warning lights I have seen go directly from the relevant sensors to the cluster and not through the ECU, as in there will be a body loom connection from the engine loom which will have all these wires and will need to be matched up. Some others are referenced like stop light signal. Warning lights from the ECU are generally Check Engine, Cat Temp (if relevant), Auto position indicators unless the Auto ECU is a separate unit.
- Crank is normally only a signal that the engine is starting to make sure it fires the injectors, ensure any Neutral Start Switch is connected if relevant (if the engine and trans are from the same donor then this will be covered in the auto connections)
- AC clutch control, again if relevant
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