I also experienced a bucking issue with partial throttle in the 5-6k rev range when my S/C was first installed. It could be a DBW/fuel delivery issue with the reflash mapping, possibly inconsistent injector spray patterns since the OEM injectors are at near max duty cycle in the higher RPMs. Unfortunately, there isn't much you can do about it. I dealt with it for over 1 1/2 years before going K-Pro. However, I never threw CELs so your problem might go deeper.
Btw, you shouldn't really need to downshift to pass someone given the great midrange you get from the S/C (especially since it sounds like you were around 4k in 5th). Old habits die hard

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