In all actuality, when you do a delete, the engine runs much cooler, gets better fuel mileage and performs better. Of course the downside is, it won't pass an emissions test. Not something I worry about myself but if you live in a test area is't a major concern.
Under warranty, I'd just let the Ford dealer deal with it and I'd get the extended warranty, the Ford Motor extended Red Carpet Warranty administrated by Ford and no other (It's listed in your owners mauual under 'warranty' and can be initiated over the phone with a call to Ford in Dearborn, Michigan.
I have it on my new Focus, not because I'm anticipating issues but because of all the electronic gizmo's. Nice thing about the Red Carpet extended warranty is when you get it, Fords immediately initiates it with ALL Ford authorized dealers so you are on file, everywhere with no hassle from any dealer. For me, it's worth the extra expense.
We happen to be a Ford family so we all drive the company product which is, neither here nor there actually but, IMO, Ford builds a quality product for the most part, however the emissions components are not Ford but other suppliers. I cannot see playing 'Russian Roulette' with components that may fail when I can buy the extended warranty and be 100% covered for the mileage and time I feel necessary.