i have the 2003 civic myself and i have done exactly the same stuff!the problem you refer is because the sensor checks the rate of your engine smoke u know and because of your mods it is more than the original presets.it doesnt affect your car at all but you can solve this with a new sensor.i left it like that and i dont really care.in fact even at the honda dealership they can fix this(i trust them more than all the other mechanics who think they can make out 200hp with whatever parts they like!)