I know that Ford has coverage on the wiring harness, but here is a word of advise. Ask to talk to the tech who is going to do the work. Offer him/her (in private) $100 to make sure the job is done right. Now you're wondering why you should pay to have warranty work done. Ford pays us about half of what the job is actually worth. On this vehicle, the pay ranges from 3.9 hours to 7.7 hours depending on how the car is equipped. It actually takes us about 6 to 10 hours to do the job. In fact, it's easier and faster to drop the engine out! So we've come up with some shortcuts. Some are good, and others not so good. So talk to the tech. Tell him you know this is a crap job. Offer to make up his lost time ($100). Tell him that you want it to look factory when it is done. I guarantee that the money will be well spent on your part. If you get a hack job done on your car, you'll waste far more than $100 on lost time with the vehicle/trying to get someone else to fix it/etc.
Take it for what it's worth...
-Greg