I work for a dealer group that owns two Mazda dealerships, called Hiley, however mine is outside of Dallas. Keeping the forum clean though, I am more than happy to take up any questions through PMs.
Ohschnapps, a swap like that would not be considered something that would be covered under warranty. What Mazda considers a warranty claim would be replacing the part, however large or small, with the same one, or an upgrade if the part is obsolete. Also, there must something wrong with the part. Your best guess may be to find a Mazda tech, and a transmission as well as all needed parts, and have him do it on the side. Therefore, he knows what he is doing and can do it in a timely fashion, and not paying the larger price that us as a dealership might charge you.