Are those torque converter codes related to any of that? Personally, I wish things were not over-designed, over the years I've known so many people to have problems as a result of torque converter lockup.
Honestly I would like to do a tune
Running an AFM deleted engine without turning it off will throw all sorts of codes. I would bet the torque converter codes are related. I would also expect abs and stabiltrack codes. Random misfire codes. Etc. I would expect all that to disappear after deactivating AFM so the ECM isn't looking for an attempting to activate the system.