Isn't emission equipment covered under warranty, I thought it was actually covered longer than the 3/36.
Try this link
http://www.ford.com/en/ourServices/shoppingAdvice/warrantiesAndExtendedServicePlans/warranties.htmSo your exhaust manifold cats are bad? or your main cat in the factory Y-pipe location.
Either way, its not too hard of a fix.
If its in your manifold it is a tough job getting to the rear cyliner bank manifold but can be done. Worst part is breaking the bolts free. Guys who are running gutted cats in there manifolds have pulled em off and those who have installed Headers have all had to pull em off. There should be a how to on making MIL eliminators to keep you CEL code off.
If its your main Cat in Y-pipe, you can replace the cat with on from the
www.summitracing.com catalog or replace the entire Y with one from SHO shop, BAT , or Performance Fords.
Hope it helps.