As I understand it, those bikes are limited release and they will sell pretty much for MSRP. I looked at Cycletrader.com, and the discounts are few, and only if you are willing to pre-pay for a bike to be delivered much later. Ride-away examples are selling for a bit over MSRP. YMMV, of course.
THE place for good FJR info is http://fjrforum.com/forum/. Register and post your question. In fact, if you poke around you'll find your exact question has and is being addressed. If you are in the SE, D&H in Cullman, AL are "the guys".
If you want to learn about FJR farkles, maint procedures, etc., check out Dale "Warchild" Wilson's http://www.fjrtech.com/
Have fun! If you do get one, let us know how it works out.
I heard there was a dealer in Alabama that has a lot of FJRs for sale and will discount them. I Bought my 2006 FJR1300AE at Destination Cyclesports in Kerrville, TX, 830-896-2453. He has two used 2005 FJRs and two new 2006 regular shift units.
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.
As stated, discounts off MSRP are few and far between unless you've pre-ordered. However, some deals are out there. I was able to pick up my '06 FJR1300A from a dealer that had a buyer back out.
Dealers are incented to move unclaimed bikes quickly as they have a pay back from mother Yamaha of $500 as long as the bike is delivered to the buyer (or a substitute) within 30 days of it arriving at the dealership.
Maybe you could wait for a while and see if Kawasaki makes good on their promise of a ZX-1400 shaftie tourer this fall. 30 more hp than the FJR, lighter, smoother, and better heat control. It should be a beaut. Also, none of this dealer presell BS.