After further research, I was wrong. All 96-04 Mustangs use versions of the 4R70W.
BUT... the bell housing pattern is different between the V6 and V8 versions. You CANNOT swap the bellhousings on the 4R70W because it is a part of the case itself. So, you will have to have a V6 version of the transmission. You can tell which is which by looking at the bolts around the starter flange, if there are 2, it's a V6 model.
Besides, the only difference as far as strength goes between the V8 and V6 models goes is a single less clutch plate in the V6 models and a difference in pressure plates. If you are worried about the performance of the transmission, check this site out: Upgrading Your AOD-E/4R70W or AOD Transmission - Baumann Electronic Controls, LLC
There are also some differences between the year models. In '98, they started using something called a "Mechanical Diode" and are actually referred to as 4R70E's because of this. So you will definitely want a '98+ if your car is '98+.
Also in mid '02, they removed the speedo gear from the tail shaft. So, if your car does not have the speedo gear, you'll want one without the speedo gear and vice versa.