I just wrapped up a weekend ride, now at ~ 1,900 miles on the 06. This bike flat out kicks ass. I'm more and more amazed with it after every ride, especially after getting to know what to expect from it on a nice road at a sport bike pace.
As far as things I'd like to improve...
I've had the same problem with the mirrors, but only on the right side. I noticed the acorn nut on the right pivot point was not cinched down as snug as the left so I gave it a turn, but I also did the 600 mile TBS at the same time, which smoothed out the vibs quite a bit around 4k rpm. It's much better now, but still not quite as clear as I'd like. Ironically, I upgraded to the FJR from a Concours, which is a fairly buzzy bike, but it's mirrors are the best I've seen on any bike.
I'll be looking for an aftermarket windshield when they become available -- I need something ~ 3.5" taller. With the stock shield, if I scrunch myself down I'm in a nice pocket with no wind noise or turbulence, perfect for listening to tunes. I'm 5'10" The width of the stock shield seems perfect.
The stock seat is ok for ~ 2-3 hrs but then I feel like I need a good stretch break. I'll probably pick up an aftermarket seat for use on multi-day trips, and continue using the stock seat for everything else.