The shafts have little clips on them that hold them into the tranny. You just have to pull on the shaft, or pry on it a little, they should pop out and be a little of a struggle to get all the way out but they will come. The easiest way would be to have someone else pull out on the hub while you pulled the axle out of the tranny.
The passenger side hafl shaft stays with the rest of the axle. There are some bolts that hold the support bearing in place, they are a little hard to get to. Once those are out the shaft will come out.
The subframe kindof aligns itself once you get it up to the right place. There is a lot of stuff that goes on or around it so take your time putting it back up so you do not pinch or smash anything.
