It looks a lot scarier than it is. Open the tailgate, remove the chrome strips (if you have them (Phillips screws)), remove the cardboard/carpet if you have it (Phillips screws), open the panel in the middle of the tailgate (all Phillips screws). That is all the access you get.
Looking at you will be the window regulator and 2 arms poking either way. You remove the window by prying up on the 2 circular spring clips at the end of those arms. Expect to destroy them; it can be tricky getting them off but my local hardward store, with a Hillman fastener center, had them in stock. Once those clips are off you can push the arms out of the lift channel and slide your window out.
I would say, open the tailgate, open the access panel and assess what you need before you really tear into it. This is not meant to be a BJs offroad sales piece, but they have some pictures and if you need this stuff, they are one place that has it all.
You will probably need the 2 side runners (these have 2 screws on the sides of the tailgate, mine were big phillips with the cog looking lock washers):
You will probably need the window scrapers (these just snap up&out, use a plastic pry bar. If you do not have a plastic prybar, get a set from Harbor Freight, they are cheap and useful like these
You MIGHT need a lift channel. I did (this just prys off the glass bottom, i used an old flathead screw driver):
If you need a lift channel you will need the gasket that holds it in (gently pound it on with a rubber mallet):
I needed the exterior switch bezel gasket (phillips screws):
I recommended these in my build (but I didn't have them so I didn't use them, if I ever open my tailgate again, which is probable, I will install them, you will have to remove the regulator to install them)
Supplies wise, you will need grease and some some cleaning supplies. I used degreaser to clean the inside of my tailgate and when the glass was out, I scrubbed the inside and hosed all the dirt out. When it was dry, I vacuumed out the bottom; it was full of rock hard rubber chunks from my factory scrapers, leaves, dirt, and some random mystery screws. I installed a tiny bit of left over sound deadener on the tailgate to hopefully quiet it down inside. I wiped down the gears of the arms and re-greased them. I did not take out my regulator because it worked fine and sounded fine before I started. You will need soapy water to install the channel on the lift bar. Bring some stiff wire brushes to clean the ground wires, connector spades, etc.
All this will make it so you glass goes up and down quietly, smoothly, and seals. If you have rattling and clunking, add this stuff to your list:
I also bypassed the safety switch on the inside of the tailgate on the driver side. I unhooked the connector, put in a jumper, wrapped it in heat shrink, coiled up the wire down below in a secure place and zip tied it down.
If you haven't read through kaiserjeep's build of Sadee, give yourself an hour or two, a comfy seat, some coffee/beer (depending on the time) and read through. There is soooo much how to in there (including the tailgate)> it is also AMAZING motivation.
More pictures in bkilby's build thread, too.
scroll down to post 467 for tailgate stuff but read the whole thing because his rig is amazing, too!
Use this thread and we can all help chip in some knowledge. It's much less complicated than you think and can be done with simple hand tools in a couple hours if you have everything with you. It can be expensive but it sure is nice when it's done!