Just got done with the clutch upgrade. The hardest part was to get the clutch boss nut off. This is a 30mm nut that's held in place by two indentations and (what looked like) red Loctite. Since I didn't have a clutch holder tool I ended up using my air impact wrench. I put the bike on the side stand, shifted in 6th gear and used the impact wrench to undo the clutch boss nut. After that it was a piece of cake. All-in-all the job took about 4 hours, but that's because I am not a professional. I needed a 30mm socket (clutch boss nut), a 5mm hex bit socket (clutch cover bolts), a 10mm socket (pressure plate bolts), a torque wrench, and a diagram of the XSR900 and FJ-09 clutch. I used most of the friction and clutch plates from the FJ-09's clutch. There are a couple of additional friction and clutch plates, which you will see on the parts diagram, which come into play in the XSR clutch and are not part of the FJ-09 clutch.
I strongly recommend having the XSR900 service manual as well. It shows how to put the plates in and the torque values for all the bolts and nuts you touch. I found a copy of it here XSR 900 Service Manual
I modified my original parts list so this is the new and tested parts list (see below). The total parts cost is around $250. Not bad at all. The thing I noticed right-away after the upgrade was how light the clutch pull is. Shifting between gears is a two fingers job now. Downshifting is so much smoother as well.
I really appreciate the light clutch pull in traffic and recommend the upgrade to all FJ-09 owners.