Let's start with the pictures: Photo Album
The shock install was a little harder than I thought but I was well prepared and it took almost 5 hours.
Start by ordering everything you need. You'll need an R6 rear shock. You'll need the shock off a 1999-2002 bike, it has the reservoir mounted horizontally, the new ones mount it vertically and it won't fit.
Next you'll need to order some brass bushings to press in to the shock mounts to make everything go back together properly. I ordered them from McMaster-Carr
Thanks to This post for the following info. Edit: The post does not exist anymore.
For the upper bushings: 2 X part # 6659 K36 Metric SAE 841 Bronze Flanged Bearing for 18mm shaft diameter, 22mm OD, 18mm length
For the lower bushings: 2 X part # 6659 K41 Metric SAE 841 Bronze Flanged Bearing for 20mm shaft diameter, 24mm OD, 16mm length
After getting the R6 shock you need to remove the bushing from the top, and the bearing from the bottom mounts. Do yourself a favour and bring it to a shop and have them press the old ones out, and the brass bushings in. I did get by using a hammer and assorted sizes of sockets though.
Figure out how the compression and rebound damping work while the shock is off the bike...
Just to prepare, read the Haynes manual on how to remove the rear shock. Basically you need to remove the fairings, exhaust pipes, the seat, the side/rear fairings, and remove the oil tank to make things easier. Also, take out the bolts holding the rear brake on. Once the swingarm is free to move, it may pull on the brake line.
After the old shock is out, you'll need the upper bushing, it will fit right into the new shock. The lower bushing was a bit tougher to get it... more on that in a bit.
The new shock has that big reservoir on it and makes it difficult to get in and out. Remove the rear wheel and rear fender to make things easy. The airbox will also have be removed.
Now, the new shock has a compression adjuster that interferes with the frame. I used a dremel and made room for it. You'll need to keep fitting the shock to find out how much to grind away. After the shock fits, then put the top bolt through, and make sure the shock can swing far enough back so the lower linkages fit. There will be some side to side movement of the shock in the upper mount, make sure that when the shock is over to the left that the shock can still swing to reach the lower mounts.
The top bolt is easy... just tighten it up. The lower is a little more difficult. The bushing didn't slide through easily for me. So I covered it in grease, got everything lined up, and started bashing it with the hammer. Then I had to give it a couple of taps from the other side to settle everything. No problem!
Once that's all together, go back and double check all the bolts are tight.
Now start putting all the other parts back on. Two things... the fender and the chain guard will need to be trimmed to make room for the reservoir. No big deal, it's just plastic. Once everything is back together double check the clearance on the reservoir to the chain guard... I had to cut it back quite a bit.
All the pictures in the album are stored in high resolution, save the file locally and zoom in to see things easier.
Ask your questions here in the comments, or use the comments on the pictures in the album.