My mods so far (the inexpensive ones) -
attach a pelican case to the tail rack, thread here: http://www.advrider.com/forums/showthread.php?t=644549
move the clutch up so my boot can easily fit under there. 5 minute process: loosen this bolt (photo taken from underneath the bike), slide clutch lever off, and put it back on where you want it. much easier to shift with offroad boots now.
install a flatland racing skid plate (about $80). use an innertube and zipties to keep it from rattling:
Cut the clutch lever shorter so that it doesn't pinch your ring and pinky fingers when you're shifting with two fingers. I cut it with a hacksaw and then used a metal file to smooth it. this will also keep the lever from breaking when you drop the bike. because you know you will. or at least, you should.
to do, and i will post pics soon... mount tool tube to side of pelican case. put new grips on, put handguards on, GPS mount/wiring, heated vest wiring, make and install small inexpensive ($5) smoke windshield (it will keep the bugs off my GPS).