I replaced my door glass due to some deep scratches. Glass scratches basically follow the same rule as paint scratches. Light ones you can actually polish out. Ones you can feel with your finger nail are not coming out without removing a significant amount of glass, inducing optical distortion, risking cracks, etc. So a replacement it is.
The glass itself is not too expensive. I think MSRP is no more than $150. You can get it for less. NCZ13 is a good source.
trim prying tools (more of a want than need)
10mm socket + wrench + extension
torque wrench good for ~10Nm
something soft to lay the door panel/glass on
First start by removing the door panel. This involves popping some plastic pieces off and two screws. You'll want to lay something soft under the door in case the panel falls. Snoopy has a great video howto here:
I used an Actron trim removal kit to get the first clips off. It looks something like this:
Unplug all of the connectors except for the window control plug. You need the window control switches in order to lower the window to gain access to the bolts holding the glass. It'll be obvious which plug it is. It connects directly behind the window control switches. You also need to disconnect the door handle latch/lock cable. You can unclip it and then it just separates from the panel.
Here is the door without the panel and all connectors disconnnected (you'll want to leave the window control plug in initially):
Once the panel is off to the side, open the black rubber weather seal covers. There's one of the left and right. They are the bigger ones on the bottom not the small ones on top.
You'll notice there's nothing behind there. This is where you need to plug in the window control connector to the door panel switches. Turn the car on but don't start it. Use the control switches to lower the window until you see the bolts through both holes.
Undo both bolts with a 10mm socket and save them. You'll need a socket extension to be able to reach far enough into the hole to the bolt. Be careful here because it's possible to drop the bolts behind the door module cover (silver thing.) You'd probably have to remove everything to get it out.
Once both bolts are out you can slide the glass upwards and out of the opening up top. Remove weather seal on the inside to allow for more clearance getting it out as there's a plastic/metal bracket that comes out attached to the glass. The seal just comes right off and is held in place by a groove.
Here is the new glass from the factory:
You'll need to transfer the white plastic piece and the metal backing to the new glass from the old one. The metal bracket comes off by using your fingers to gently lift the clips to the side and pulling the metal piece upwards.
The plastic piece is a folding bracket that clips into itself through the hole. Be gently when unclipping it to avoid breaking it.
Once the pieces have been transferred you can lower the new glass back into the door slot where it came out. It might take some wiggling to get it back in. Just be gentle. There's no need to force anything. If it won't go in try another angle.
The glass will then sit back in the metal frame holder you can see through the holes. If the bolt holes don't line up just lift the glass and move it over until they are. Then reattach the bolts. Try and tighten them so that they overlap the 'impressions' in the metal that were there before. This will get you close to where the window will finally be adjusted to. Tighten to no more than 8.8-11.8 Nm. You don't want to crack/shatter the glass from overtightening.
Once the glass is in place connect the door panel switches again and use them to raise the window as far as it will go. Then remove the door panel again.
Close the door and the glass will 'scoot' up to seal against the weather stripping. Check the gap.
On my first try the gap was too big towards the front:
If the gap between the glass the seal is not even all the way across you need to open the door, use the door panel switch to lower the glass until you can see the bolts, then adjust the glass by loosening the bolts and gently adjusting the glass position. Tighten to spec, raise the glass, and then close the door. Check the gap again. Repeat this process until the gaps are even and the window seals are good.
The service manual calls for using a hose to test for leaks. I didn't so I made sure the window glass snugged up against the seals at all points. You'll see the seals move as the glass presses against them. That should be good enough. It's not like the manual called for anything scientific anyway. They recommend using a hose, setting the water height, and then pointing it at the glass from 12 inches away.
Here are the final gaps:
Once you've gotten the gaps good, make sure the glass bolts are torqued to spec. Close up the rubber hole seals. Reattach the door panel/connector plugs/door latch cable. Finally, check to see whether the door handle works from the inside. Make sure the lock works and the windows work.
If everything checks out you're all done.