I would say put the old air box back on if you have it. If not see if you can get one. I think unless they can prove it caused the problem they can't refuse to fix it under warrenty. But it is just better to not tell them about it or let them see it on there.
Is the car running OK? I bet it is just an O2 sensor giving a false reading. I had one go out on me just after getting the car. Now I have a bad one (Or more?) from when I blew the head gasket on the car. It is not a big deal, the only thing it might do is your gas milage may go down a little. I get about 300-310 miles on a tank of gas when the sensors are good. But now both times my O2 sensors have gone out I get about 275-280 at most.
What dealer are you going to take it to? Any suggestions? I bought my car used, but have some recall work to be done. I took my car to McKay Licoln Mercury once, not sure if I liked them or if they just had a bad day. Their guy said my breaks were ok, and their bid was on the high side. Took it to Midas down the road, he said I had less than 10% breaking power left. (Had to go to McKay to get my wheels off. Locking nuts, but never get the key. Glad I didn't have a flat before then.)
