Did you try resetting the ECU? It could potentially have just been the ECU adjusting to the CBE however the misfire is a bit strange as I doubt a CBE would ever cause it to misfire.
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-320whp / 259wftlbs-
SP Rays -- RE-11s -- SpecialtyZ Tune -- Swift Springs -- Stillen 25R Oil Cooler -- Stillen G3 Intakes -- Berk HFCs -- F.I. 12" CBE -- Stillen Sway Bars -- Es14 Spring -- INGS+1 lip -- CF Spoiler -- GTR Start Button -- VLED Parking Lights -- PWJDM V2 shift knob
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