For a quality rebuild, you are looking at anywhere from $2000-$3000. A Ford rebuilt tranny with a 12/12 warranty (recently reported to be longer now, but is valid at every Ford dealer in the world) is about $1700 PLUS labor. Book labor is about 6 hours, so if your Ford dealer charges $100/hour labor, you'd be looking at around $2300. FPS in Georgia will ship you a rebuilt tranny for about $2200, plus core charge, plus round-trip shipping, plus labor, but if you just drive it as a daily driver it's probably not worth the extra $$$ for their high-performance tranny.
You could also try to find a local shop that rebuilds trannys (this does NOT mean AAMCO!!!), but try to find one with a lot of Ford FWD experience, even better if they have SHO experience. It will probably be the least expensive option, but also the most prone to problems requiring return visits so make sure there is a comprehensive warranty and check them with the BBB, etc.