3.8 Tranny

Hey everybody, new to the forum. I have a 2000 V-6 3.8. I am in the market for a new tranny(blown) I've got about 90k on her. Does anyone know what I can put in? Would a 4.6 GT, or Cobra fit? Any other upgrade ideas since I have to replace it anyway? Thanks a lot everyone. Hope to hear back.

-Chris, (stuck and confused)