Some good news, but first an odd twist in the story:
As my sister wanted to fix this issue asap, when she was at the ford dealer, a member of this particular dealership informed her that he runs a muffler shop and he could do the work for her out side the dealer for half price. My sister said ok, and had put down a $400 deposit with the muffler shop.
Last night i spoke to her and informed her of the information provided here by you good folks, I told her to get to the dealership first thing in the morning and open this issue up with the 8 year 80,000 mile warranty right away before it's too late. Ford dealer apologized and said they had entered one number wrong into the computer so that it didn't show this warranty for her. Wow!
Whether honest mistake or not, i don't know i am not dealing in person with them. So i can't say. She has cancelled with the muffler shop.
Moving on, they are going to replace cat cons under warranty, no charge. And begin looking into the cause-hope this turns out to be positive and not another challenge.