You are looking at one SWEET motorcycle, my friend!
Deals are difficult to come by.
I live in the St Louis area and went to Donelson Cycles, our biggest Yamaha dealer. They quoted me a price of over $14,100 out the door for a new 2006 model.
I looked in Effingham, IL at a 2005 model that was $13,500. It was on the floor because a guy had backed out of his order.
The guys are right on in answering that Yamaha has a program called, "PDP" or something which requires you to make a deposit of $500 and wait for your bike to come from Japan.
Alternatively, you can do what I did, which was join the FJR Forum, look for people selling, and go get it! I drove to KC in Feb to pick up a 2005 model that had over 12,000 miles on it. Got a great deal. It's been a fantastic bike! Don't let the rarity of this bike deter you. Once you find one and get on it, you'll know why some people call it one of the most desirable motorcycles on the market.