I am running a Fi2000R tuner and also have the cobra proflo air intake- current settings are a 2.5, 6, 6. I spoke to Cobra about the bike stuttering/hesitating and they recommended that I adjust the pods 1/2 turn at a time. The bike still is not running the way I wish so I ordered the CVT tuner. I am working with my dealership to get a credit on the FI200R, but as of right now it looks like I am going to eat the $250 for the Fi2000R.
My recommendation to you would be to keep adjusting it 1/2 a turn until it comes around. Make sure to put some miles on it between adjustments though, the bike needs time to react to the change in the tune.