Remove the shift linkage rod from the shift shaft by removing the 10mm bolt in the linkage arm. You can let this hang free without removing the remainder of the shifter assembly.
Now that you have the clutch slave cylinder out of the way you can actually get to the cover under which is the shifting parts. Unplug the single wire connector going to the center of this cover (the neutral light circuit) and move this wire out of the way.

Put something on the ground to catch some of the oil that is trapped in this section even though you drained the crankcase. Probably a cup of oil, give or take a little bit.

Using a suitable 8mm socket remove the 6 bolts holding this cover. Take note that not all of the bolts are the same length so you will need to pay attention to which one's are coming out of which holes.
 
You should now be looking at something like this. There is a snap ring on the shaft that you do not need to remove unless you are going to replace the spring behind it. I removed it, turned out I didn't need to, but I didn't know any better. Snap ring pliers are a must if your planning on removing them (Autozone, $11.99 and took me about 30 minutes to go to town and get them).

That big lug looking thing in the middle takes a #5 metric Allen wrench to remove. Once you take that center Allen bolt out you can now remove pretty much the whole assembly, shaft and all. Watch on the back of the shaft as it comes out of the crankcase hole, there is a small thin washer.

Continued...