I recently bought a truck with a few issues. The motor starts easy, sounds good and runs strong. It has some dead pedal and shifting problems and the previous owner said it needed an APPS. After replacing the APPS symptoms are different but still present. The code reader at Auto Zone said it has a PCM failure. Being as this is a 2nd engine truck, should I take the PCM to the dealership and have it re-flashed to see if this solves my problems or just try to find another one? If I was to try to find one in a junkyard, is it enough to match year model, trans type and 4 wheel drive or would it still need to be flashed?

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1998 2500 24V automatic 4x4 2nd motor. Stock