We don't get involved with costs here because there's way too many variables. Labor rates vary a lot, and the cost at one shop can vary widely depending on whether it's a simple rebuild with a new clutch plate and gasket set or if other major parts need to be replaced.
It is also more common to have a rebuilt transmission installed for a set price, then your old one is shipped back to be rebuilt and sold to the next person, kind of like reusing pop bottles.
There are a few Ford transmissions that are REAL expensive to rebuild and real expensive to buy rebuilt ones. In particular there is one model of manual transmission that costs a lot. You didn't say whether you have an automatic or manual, or what's wrong with it, so these are just generalizations.
Usually you'll get a better price from an independent transmission shop but often they will elect to rebuild your transmission which takes longer, but that way if no expensive internal parts are needed, it will cost you less.