What do i do if my cars ecu does not reset itself?

I just installed a cold air intake on my 2000, 2.4 mitsubishi eclipse and i love the boost, but my ecu will not reset itself which in turn, makes the car sputter while idling and lurch while driving. I've tried disconnecting the battery for hours and gone on more than a 10 mile drive, but it still will not make a difference. what do i do???