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Legacy manual swap


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I just purchased an automatic 2002 legacy l wagon to replace my daily that got totaled. I have a manual 1996 legacy wagon with engine and body issues. I am a mechanic and can do the physical trans swap easily, but I am concerned about the engine starting and running correctly without input from the transmission. Is it possible to use the 96 ecu to avoid issues or is there a better way to accomplish this?
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I haven't done it, but I believe that trans harness swap involves making sure a particular wire is grounded or not or maybe a loop closed or not. That tells the ECU if it is manual or auto. There are references to it around here somewhere. That is to say, the ECU is the same and there is a wire signal to tell it whether to talk to a TCU or not.
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