In my past experience doing 2 T5 swaps into 5.7L Firebird GTA's, the car will run, but will also give you some problems with the auto computer. Yes, these are 2 different cars but just some possible problems you might encounter. The most noticleable problem was that at the very high end, the car would fall on its face. Not sure why, maybe because the car is set to shift the auto at a certain RPM and I was well over that mark. But that was a problem I noticed that was never there with it was an automatic. Hope you are handy with a jigsaw too, you will need it to install the clutch pedal.
clutch pedal requires no cutting, pure bolt in. Auto tranny function can be turned off with custom tune, however, the only side affect from not turning them off is a check engine light. just because one car does one thing, doesnt mean it holds true for a stang.