Actually the reason why it throws the P0888 code is because all the stage 3 PCMs are derived from automatic PT Cruiser PCMs. The PCM is looking for a signal from the automatic transmission, and since there isn’t one in the SRT-4 it throws the code. This car has the code scrubber and has passed NY inspection many times with Stage 3 installed.
Stage 1 and 2 are also “off road use only”, but use PCMs derived from the SRT-4, thats why there is no P0888 code with Stage 1 or 2.