I believe the ecu is a closed loop system and won't compensate for the increased free breathing.
Yet, I'm not running a Power Commander, have'nt had re-mapping done, and it runs fine, not popping on deceleration, no flat spots/hesitation, surging or anything that I can tell would mean it's lean. My plugs and exhaust look fine, definately towards the leaner side, but not lean. I'm sure doing the above would help, but it seems to be right at the fine line of needing to do that. If there was a proven map for my setup (open airbox, K&N filter, Sebring Twister w/baffles in/out, gearing change etc, I would probably do it, but being there's not, I'm not into buying a Power Commander and flogging it on a dyno.....for now. Maybe someday