Muffler delete adjustment

[Slickr1023]

I recently removed the 2 factory mufflers and replaced them with 2.5" straight piping, the car ran poorly after that change. The car would stutter and knock under acceleration depending on how sudden I hit the throttle, a couple of other thing contributed as detailed here viewtopic.php?f=50&t=22230, but I believe my muffler delete contributed to the problem because I subsequently loaded a +3psi calibration (international NO/CARB) with the 'Disable Secondary o2' Mod and now the car runs fine. Was this the fix for the muffler delete or did it remedy some other problem? Also, I don't want to hurt the catalytic converter and possibly gas mileage, so is there a tune adjustment that can be made to incorporate the functioning of the secondary o2 sensor?

[Hondata]

Removing the mufflers makes no tuning difference. From your other posts you fuel trims are -15% and AFR under 10:1 so I'd look at the AFM first.