If my automatic was going out I'd be glad and switch over to a T5 which is the standard 5 speed transmission for the 2.3L cars. Used T5s are very inexpensive, plus you can buy tranny rebuild parts off of summit racing.
Call up a local junk yard and see if you can price one that comes with a warranty, the transmissions from the big name parts dealers come with 3 year warrantys usually but they are quite a bit more expensive in comparison to the junk yard ones, since they are rebuild/refurb.
Or if you hate your car now is a good time to put a sizable down payment on a newer model Mustang haha.
But if you like your car then, you'll like the performance you get out of your Mustang after a manual switch over. Its nothing to write home about, but your driving experience will be more enjoyable in my opinion.