Don't quote me on this, but doesn't the PCIII just piggyback to the factory ECU?
I am fairly sure that the stock ECU has an ability to determine altitude and adjust accordingly. If true, then the stock ECU will make the adjustment and the PCIII will then modify the stock unit's MAP as it always has. Therefore, the difference in altitude will have very little effect on performance. I guess you could argue that a marginal gain might be had by retuning the PCIII but it would not be worth the cost to all but the most serious riders.
HTH,
rick
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