I heard issues ranging from the cat converter cracking to faulty exhaust manifold gaskets. Curious to see if Ford would void my warranty if I put on an aftermarket. I would hate for them to come back and say "the reason your turbo crapped out is caused by the aftermarket exhaust."
Answering your original question depends entirely on the circumstances. I will say that if your local performance-oriented Ford dealer puts the aftermarket cats on- you're probably good. If you do it yourself or at an aftermarket shop, you'll be taking a chance. I'm not judging, but you do know it's a federal offense to modify working emission equipment without the correct supporting documentation, right? Luckily you don't normally see EPA officers trying to trap individuals, but if your local Ford dealer decides there's not enough recompense to deal with the side effects of your modifications or the warranty rep decides it's too much of a cost to Ford to repair under warranty because of your mods, you have a problem.
As I posted in other threads, if you modify your car, you assume some responsibility- pay to play. And for those who are going to scream about Magnuson-Moss et al, and their rights, when your dealership decides to not warranty the repair, unless it's egregious, are you really going to let your car sit idle while you hire a lawyer and start the proceedings? Just an FYI.
