There are several ways to do this but it will not be too easy depending on how close to a factory automatic car you are trying to get. If you are planning on installing a C4 or an AOD you can disregard any computer or wiring concerns. But, you will have trouble getting the speedo to work (older transmissions use gears to drive a mechanical speedometer, newer transmissions use a sensor with an electronic speedometer). If you choose to install the correct transmission for that year car (probably a 4R70w), you will run into lots of obstacles doing this swap; the wiring and computer being the two most formidable. You can solve the wiring issue by swapping out the harness. I think there is a seperate transmission harness that you can change. You will also need to replace the computer with the correct one for both your car and the trans (Engine, transmission, and year). You might also be able to run a standalone TCM. You can find them online.
But, I think the biggest question is how much work and money are you williing to put into this. Be advised, this will be lots of work. You will need to take apart the dash and most of the interior in addition to the mechanical portions. It will also cost you a lot. That also doesn't take into consideration the programming work and the vehicle system gremlins that are sure to pop up. Bottom line is, if you just want an automatic Mustang, I would suggest just buying one that came as an automatic. Ford made a ton of them and you could probably find someone who would swap you for your car. I for one can say I would rather have a manual transmission then an auto. I have three automatic Mustangs that I would like better as manuals. Now if you are building a drag car, then an auto is a better way to go; especially when you get into a very high-horsepower car. Anything that runs more than a 12 second 1/4 mile would be better with a manual anyway.
Well, not sure if this helps or not. Good luck.