Don't be mean.
You asked for help and you got some.
There is nothing really complicated about removing the transmission. You just unbolt everything that needs to be undone in order to get it loose from the engine and the truck.
It is a bit more difficult to put back in as you have to get it lined up.
You need to remove the shifters from inside.
You need to disconnect wiring from the transmission under the truck. You should start by disconnecting the battery too.
You will need to lift the truck a bit but not a whole lot. Make sure you have it securely on jack stands so you don't kill yourself.
You will need a transmission jack. I used one of the scissor style units as I did not have enough height to permit the use of one of the adaptors that sits in the saddle of the floor jack. I did not want to lift the truck that much.
The transmission and the transfer case come out as one unit. It is very heavy and off balance so be careful. You do not want to attempt it without a transmission jack and it needs to be tied to the jack so it cannot fall on you.
Remove all of the bolts from the bellhousing, or at least loosen all of them and leave a couple in until you are ready to actually remove the transmission. As already noted a flex socket and a long extension are going to be needed for the upper bolts as there is not a whole lot of space in there.
Once you have most of the stuff loose - but the bolts not all removed, support the transmission and then remove the rear crossmember that holds the back of the transmission.
You will have removed the drive shafts, front and back by then and hopefully you remembered to mark them so you can put them back as they came out. I normally wipe them off and then spray a line on the unit with a paint can before removing them. An orange or white stripe will show you how they go back together. Some people will mark them with a punch etc. To each his own.
After the cross member comes off and you have removed the last bolts on the bell housing you should be able to wiggle the transmission back and then once the input shaft is clear of the clutch, lower it down. At this point, I had to then slide the transmission off of the jack in order to get enough clearance to drag it out from under the truck.
You will then be able to get at the flywheel.
Let me suggest that you have a good look and replace anything else in the clutch setup that needs it now as taking this thing apart often is not my idea of fun. I have had the transmission out of our 95 4Runner 3 times. If the clutch is worn, do yourself a favour and put a new one in. Get one from Toyota. I had no luck with aftermarket kits and that is one of the reasons for my having it apart so many times.
If you are feeling poor and the pressure plate looks reasonable and is flat, you might get away with just the clutch disk itself. Get one from Toyota! They are not expensive. I would also at a minumum replace the throw out bearing and the bearing in the end of the crank. Find a wooden dowel that fits it tight - fill the hole with grease - then pound the dowel into the grease and the bearing will come out. Gently tap the new one in using a socket of the right size.
If you pull the pressure plate off, which you will I guess if you are going to swap out the flywheel, then you will need an alignment tool to put it back correctly so you can get the input shaft back into the hole.
When you are ready to put it back in, make yourself some alignment dowels from bolts with the heads cut off. I got the right sized bolts from some place like Home Depot and cut the heads off and cut slots for a screwdriver (so I could get them out again) and then put them in a hole on each side of the engine to help align the bellhousing when the transmission goes back in. Get 2 helpers to put it back. One to lay under the front and tell you when it is lined up or help shift it into place and one of you on either side of the transmission further back to work the jack for lift and to wiggle the thing back into place. As I said, with the transfer case hanging on one side it is not evenly balanced and thus needs to be helped into place.
Once the transmission is back in place, it is a simple matter of replacing everything you removed or disconnected.
It is heavy. Be careful.
There is also this
http://www.4x4wire.com/toyota/4Runner/maintenance/clutch/and although it relates to a newer vehicle, it is essentially the same.
Randy