to my understanding, it is better that you swap the complete engine along with the auto transmission, because of the consumption, pick-up sacrifice you may have to give if you mate an auto transmission with current engine..
on the other hand if u look at the registration and engine number changing hassle on reg book, its acceptable that u mate an auto gear box with your current set up.
but what ever u do, just be assured that you are NOT putting in a CNG once its auto transmission...