What are you hoping to accomplish by changeing your shif points? If you are having a problem that changing the shift points will cure, then your PCM is covered for 8 years / 80K miles. If you are under those limits, Ford will re-flash it at no charge under warranty. I had mine re-flashed at 50K miles under warranty to cure a hesitation problem I was experiencing.
If you are outside of the PCM warranty and are experiencing problems, then figure on about one hour of labor. In my area, Ford charges about $72/hour. It will only take them about ten minutes to do, but they like to stick to the one hour charge.
If you are looking for firmer shifts, I doubt if you can get Ford to do it. They may not even have the knowledge or ability to do it. Anytime they put a new program into the PCM, it has to meet strict emissions standards. They are supposed to put a "vehicle modification" sticker on your vehicle to indicate that they modified your PCM. If Ford would feel that by making your shifts firmer it would increase your emissions, then they won't do it. If you want firmer shifts, a Superchip will do that for about $200.