At about 2,000 miles on the odometer, I decelerated from 60 coming into a town. I took this opportunity to stretch a little bit and took one hand off the bars, loosely gripping the bar with my other hand. As I my speed decreased through about 40 mph, the handlebars started shaking back and forth. As soon as I placed my other hand back on the bar, it stopped being as violent, but I quickly found a place to pull over. I was sure that I had a flat tire.
Upon inspection, however, there was nothing wrong with the tire. Hoping back on the road, i began to experiment, and discovered that while decelerating through about 40 mph with a light touch on the bars would cause a violent front end wobble. As soon as the speed was below about 35, it would go a way. It also didn't happen during accelleration.
Once home, I asked my father-in-law about this, and he (along with many other people on the internet who have had this problem) thought it was due to loose front steering bearing. I also talked with fellow FJR rider Bill Lynes and found he also had this problem. His theory was that it was the stock tires on the FJR. As soon as he switched to Michelin PR4s, the problem went away.
Another theory I read was that the problem was caused by the stock Bridgestones in combined with low air pressure. I checked my air pressures and they were down slightly, but only like a pound or two. Nothing major. Since I was getting a small amount of cupping on the rear wheel, I decided to increase the air pressure on both wheels and took it for a ride.
Changing the air pressure COMPLETELY solved this problem. I was amazed and a little releaved that I didn't have to disassemble the front end to deal with the bearing!