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And both those symptoms point toward the ECU connection on the side of the engine… the service brake switch sends a signal to the ECU on the side of the engine, which puts that information out onto the data bus(Not sure if the trans uses brake info though). The high idle command switch feeds...
You said that fault was for comms between transmission and engine. Have you checked the connections at the engine control unit? Is the inline filter module still installed at the ECU?