The only thing that needs programmed is the diesel pump, if you get your mechanic or yourself if your doing it to change over the diesel pump it will be fine. You will need the timing pins etc tho to do this as you will have to take the chain off at the bottom.

I think its quite expensive to pay ford to reprogramme it. I changed same engine as the focus on a wee fiesta that did the bottom end in and changed pump with old one and it started fine.