With a tranny problem, an axle (cv joint??) problem, and a clunking noise (strut problem??), I would suggest trying to make all of those repairs at the same time. It's hard enough to pull the struts/axles/transmission out of the car, and you don't want to pull everything for one repair and then turn around a week or a month later and pull everything again. Been there, done that. Also, check your ball joints while you're in there. Putting in new ball joints will make the axle/strut replacement (if they need replaced) much easier.
