I don't understand why everyone automatically went to they should by it back? Did you even ask for some sort of compensation or did they offer it to you? I don't work for Mazda or any Mazda dealership, but its not like the dealer and corperate aren't trying to make things right or denying anything here. They are doing exactly what needs to be done. It's not like overnighting a trans from Japan is a cheap thing to do. It's going to have to go through customs which will also take some time (a day or two). Also when the dealer got corperate involved that also takes time for their rep to schedule to get to the dealer and make the final word as to what they are going to do. Add to it being a newer model that parts aren't readily avialable its understandable that they can't fix a trans problem right away. At least you are getting a brand new trans, not having yours rebuilt or getting a factory rebuild (which is also a reason why its taking some time cause they have to pull one from the assembly line). Plus the dealer is warrantying an alignment is pretty rare. I've driven Chicago roads and they are quite pot hole filled which can easily alter your alignment if you hit one hard enough.
Also lemon law only works if the car is down for over 30 days, or has the same exact problem 4 times. That doesn't mean that I had a check engine light 4 times so buy it back. If it had 4 different faults it doesn't count cause they consider that 4 seperate problems. If it was the same exact fault 4 times in a row then that is considered a lemon law situation.