Hi,
No I did not have any aftermarket items on my car. The only problem you might run into when replacing the exhuast and intake with NEW stock ones, is that the Honda dealership will probably notice that you have a brand new exhuast and intake. I am sure they have run into this situation before. They might call you out on the late swap, and recognize you replaced these parts inorder to qualify for warranty coverage on the Cat. Sorry if this sounds depressing but I am just trying to brain storm. Again, good luck.