With some ECU's, you can take them to a company that does automotive computer work, and have it re-programmed with the necessary information to function with the new transmission. If the ECU cannot be reprogrammed, then it might need to be replaced with one that has the parameters needed to operate the engine with the different transmission.
If the car had the option of manual or automatic, you can take the computer out of the donor vehicle, and it should work with your car. You might need to have it flashed (by a place that can program automotive computers) for it to accept the your car; especially if the car has a different engine or is of a different year or model.
If the car never had the option of a manual transmission, and you are swapping something in from a completely different vehicle, then you might not be able reprogram the computer. You might be able to find a replacement ECU from an aftermarket supplier, which may be able to operate the engine correctly
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