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The curiosity is if you can use a variety of factory ecu's and run another engine from it, such as using the ecm in a jaguar v8 car to run an American LS?
People do try things like this, but its a very complex way and doesn't always work due to hardware limitations. People have cracked certain OEM ecu's platforms really deeply and it's not impossible but it's unlikely to work.
The universal solution is a standalone ECU. If you're worried about the CAN data keeping the factory systems happy, you can run the ecu's in parallel or find a company/person who has the OEM CAN data in their calibration and is willing to sell it.
I can't be more specific then that without more info