As you're experiencing, anything more than a catback exhaust is asking for trouble during warranty. Especially in lean times like this. And not putting car back to OEM before taking it in is also a bad idea. Anyway, I've heard about resonator delete, but never cutting slits on exhaust pipes man. Who the heck convinced you to do that?
Bottom line is this. I doubt what you're describing can cause engine damage, but if a jury was to decide your case, I bet at least 95 out of 100 potential jurors would side with the dealer. You'd need an expert to convince the jury otherwise, and I doubt there're any exhaust 'slit' experts around. Consider yourself lucky your dad works there, and just follow his advice. Do you have anything else done to the car, like a tune? Keep us posted what dealer finds.