The EPA mandated warranty on emissions items (PCM & cats for sure, various other sensors on different models, typically O2s) is 8 years 80,000 miles on all vehicles that age. That took effect in 2003 (for the 2003 or 2004 model year one, which I'm not sure) if I'm not mistaken, before that it was 5 years 50k.
Dealer could clear it up for you and you can give us the specifics I'm unsure of. But I'm 100% sure that cats are covered in that warranty for 8/80 on your '07.
One thing I'm unsure of, whether the EPA makes them change it just cause it is rattling, or only if it isn't functioning. They may try to dodge the repair if they can test the emissions at the exhaust and the cat is working seeing as Ford eats the cost on such items, and if they test the cat and it works, they force the dealer to eat it.
The exhaust on these engines flows plenty well enough to exhaust everything the engine breathes in. The difference going to high flow cats would be minimal. I have no idea of the cost.
P.S. running with a miss and really really realy bad gas is the only ways I know of killing a cat...