I just wrapped up a weekend ride, now at ~ 1,900 miles on the 06. This bike flat out kicks ***. 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.