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Does any of these parameters change for configuring a base tune file for a new cam when a manual transmission is involved instead of automatic?
Does the ECU interact with a transmission controller for the automatic? Unless it does I wouldn't consider any changes required.
From my experience with Evos and Airtreks (sharing the same engine but different transmissions) the same turbo would spool up quicker ( around 500 RPM) when on automatic transmission. So ignition timing and fuel tables should be adjusted to reflect it...
