As seemingly always, this topic is kind of half covered. I am going to see if I can do a little better. The op wrote:
"Manual says:
Remove the exhaust muffler
Remove the brake caliper
Remove the rear fork
Remove rear axle collar"
So now that I have done it, here is the REAL scoop with a couple of pictures....
1) detach the exhaust muffler. The first thing to do is to take off the top/front muffler cover to expose the muffler attach points. Once off, take off the two nuts holding the muffler to the engine. (if you dont, and go ahead and detach the muffler points that were up under the cover, the muffler will be hanging by that little tube. you dont want that). Now take off the three bolts holding on the muffler, and gently pull the whole thing away from the engine. You will not be able to pull it out because there is still an oxygen sensor attached, so I just laid it to the side. Also, there is a crush washer between the muffler and the engine, and it will fall out when you remove the muffler. Don't miss that washer!
2) I took off the seat and took out the tub. As it turns out, I did not see a way of getting the wheel past the right side spring, so I took off the seat/tub to be able to detach the spring from the top. I also intend on running power lines to the front glove box, so I needed to do it anyway.
3) detach right side spring and set aside. if you have the tub out, come into that top nut from below/behind and remove it. The spring assembly will drop out.
4) take off the fender bolts. There are three little 10mm bolts holding on the fender. The fender will still be stuck up in there with the wheel, but the whole thing will slide with the wheel when you pull the wheel.
5) detach the brake bolts, and pull the brake off of the rotor. Jam a few thicknesses of cardboard in the gap where the rotor was to keep anyone from accidentally squeezing the brake and causing you a problem later. Besides the spring mount, there are two more bolts holding on the Y plate at the top right and bottom right. Remove those bolts. At the point, the whole "Y" plate holding the brake can be slid off and laid to the side with the muffler. the brake hose is still attached.
6) Take off the big bolt holding on the wheel. I have an impact wrench and compressor. I did not have to hold it or anything, just put it on the bolt and it spun off in a few seconds. Note that there is a big spacer and the wide end it toward the bike.
At this point the whole wheel can be pulled off the bike. the fender will come off with it.