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No not to that extreme for the cam phasers. Try the auto ecu with the automatic disabled and delete any codes that come on.

We usually lock out the phasers or limit them. Try setting engine>torque management>general>torque intervention- to disable. It might have a signal from the auto harness for a wire that isn't in the...

I had problems once with a trans swap but it was with another software and the equizzer settings in the ecu. The car had way different issues. Can you post the file from the auto car. Maybe there are...

Check the wiring for the sensors if their okay then start looking at the tune. Was the only thing you changed the transmission before the problem happened? No fault codes stored in the ecu? Have you...

Can you attach the log file and tune file? There is a few things that can cut spark so it is hard to tell what is causing it from the picture you posted you can just see that it is pulling timing.