I have done a couple of auto to manual mods. The latest of which was a w58 tranny swap on a lexus sc400 (I finished right before I sold it). I tried to sell it before for 5k but no takers. As soon as I finished it, I sold it for 12K! So for that car, yes it was worth it.
On the other hand, mustangs are very popular and manuals are very easy to come by unlike a manual Lexus SC400 1uzfe.
I don't entirely think that it would be "worth it" for the swap. It can be extremely complicated (esp when your trying to fit the pedal...) and it could very well cost you more than selling yours, buying a manual and having a rebuild on the tranny.
Hope this is useful for you?