Transfer case stays. Check it for leaks while you are under there though. I drive onto a couple ramps and floor jack the back or you could go with all jack stands. What I do is get a bungie cord or two to hold the front drive shaft out of the way as well as the exhaust pipe. I disconnect the exhaust between the cat and the muffler and swing it to the side and secure it with a bungie. Disconnect the clutch cable and secure to the side. Careful not to mess up the clutch cable. Disconnect the neg from the battery. unbolt the starter and secure it. You don't have to fully remove it but you can. I just unbolt it and secure it.
It is helpful to have a bottle jack handle about 20 inches long to jam under the transmission when you are putting it back on as well as dropping it. I always wedge it between the frame spots that are by the transmission for when my arms get tired. I also use a pair of vice grips
lightly attached to the splines at the back of the transmission to help turn it to line up the splines that go in the pilot bushing.
Disconnect the two plugs from behind the distributor that connect to the wires coming out of the transmission. Don't ruin them because the switches aren't cheap. One's the backup light switch and the other is a modulator valve switch of some sort that has to do with the stock carburetor. It can be sold but the hole in the transmission still has to be plugged.
Put the transmission in neutral. Remove the stick shift. Next, drain the transmission, and unbolt it. Remove the support bar (two 14 millimeter bolts.)
Now here's where I catch hell here. I support the engine from above (come along to a chain attached to a bolt in the ceiling) and unbolt the motor mounts from the frame and slide the engine forward a couple inches. Then disconnect the transmission mount and pull the transmission back, tilt it forward and remove it. Now clean the outside off really good to save time later. You could sand blast it to look like new but don't get any sand in it. Most important is to make sure that any rusty bolts get pb blasted if they don't want to let loose. Also, you are dealing with aluminum so don't over torque on reassembly on aluminum threads or you can easily strip them. Keep track of what bolts went where and what direction exhaust hangers and such reattach.
As far as the tranny, get a nice big table with a towel or two to lay out your parts. I hope you have the right pullers and pipes and stuff to get all of it apart and back together. I would help you out but I'm a good 1000 miles away. Watch the orientation of the synchros, shift collars etc. Basically, lay it out in
PERFECT ORDER.
The rest will be the learning experience.
I hope I haven't forgot anything. The reason I undo the motor mounts is it gives good clearance plus the first time I did a tranny on a samurai, I broke a motor mount. Some of these methods may be unorthodox but have worked for me all 4 or 5 times I have had my transmission out since the first time on the Samurai.
Just take your time, be careful and use your head.
I've done clutches before drunk but it's better to do the drinking afterwards so you don't mess anything up.
Hope that helps.
-Adam