The fact that it went away and then came back must have some bearing on the problem. I suspect a sensor issue and/or associated wiring. I would double check everything and in particular earthing. Disconnecting the battery may be a red herring - I had plenty of those when trying to diagnose my misfire last year.
Some sensors are "optional" with the ECU reverting to default values. If you know/can find out which sensors are optional I would start by disconnecting them.
Cheers, Robin
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