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Yes, it will matter. The S has different valvetrain specs. Your best bet will be to get a custom map made. I tried just about all the "free" maps for my 749 w/ 54mm Termi, and none worked better than stock. I did find that the "trimmed" stock ECU worked better than the uncorrected DP ecu.

You shouldnt need a PCIII for the slipon. You can adjust the CO trim (with a Mathesis) to make the base map richer overall.
 
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