I like my FJR very much. It has met or exceeded my expectations in most every way. That is not to say that it is perfect, it is not, but none are.
Vibrations issues: You will sense some vibrations coming throught the bars but it is much different than on a HD. I have been riding mostly I4's all of my riding years and the FJR vibrations are much less than other I4's I have owned, or ridden. I also ride a V-twin, a 90 degree V-twin or more properly
an L-twin.
Being a 90 degree it is naturally balanced and the vibrations on that are negligable except at idle so it is not a good comparison to your Soft Tail but I have been on a few HD's and the vibes on a FJR are much different, you may not even notice them.
Gearing is fine. The acceleration is very good for a big bike. If you have not been on a powerful I4 you may find it a bit intimidating at first but you will get to lust it after a few hours in the saddle. In 5th gear you can cruise easily at 100+ MPH if you can get away with it.
Handling: It handles exceptionally well for a big bike, my other bike is sport bike and it is no comparison to that but, it handles very nicely for a sport touring bike. This would be a tall engineering order but I think the Yamaha engineers could enhance the handling by carrying the fuel lower in the frame to lower it's center of gravity. The bike has a slight top heavy feel at slow speeds.
Comfort: The bike is very comfortable for my frame. I have two compaints on comfort. The throttle return spring is too strong for a long distance motorcycle.
You can find several fixes for that using the search function on this web site. I also found that the stock seat rubbed my urethra the wrong way. After a few hours I was skirming in the seat. I got a Corbin seat and no more problems and the Corbin also lowered my seat height by an 1" or so which worked out very well for my challenged inseam length. As far as comfort goes, I rode my FJR from Enfield, CT to Denver CO nonstop (except for fuel, food, ect). 1900 miles in 32.5 hours. I am not recommending this but it is a testement to it's comfort and rideability. Something Yamaha should address is self cancelling turn signals. I had them on my 1980 Suzuki GS1000G.
Braking: This bike brakes exceptionally well for a bike of it's heft. I have an 06 which is an ABS and the braking is very linear but firm and strong.
Build quality seems fine, I have no complaints. It is a quality motorcycle. The welds on the frame seem better/more precise than on my Suzuki.
Overview: I would buy this bike again in a second. It has worked out near perfectly for me and my tastes in a touring motorcycle of a sporting nature.
Other bikes I looked at when I was looking. Ducati ST4 (I like 90 degree V-twins) Triumph ST ( I liked the 3-cyl engine and the look) and the FJR.
I was not interested in a Gold Wing, it is a little too over the top for me, kind of like riding the livingroom around.
Obviously I bought the FJR and I am totally confident that I made the correct decision. I see myself holding onto to this bike for several years because I LIKE it!
I think my worst experience with buying/owning this bike was the purchase process commonly called the PDP plan. That whole process was frustrating for me and many others on this site, but you get over it soon after you drive your bike away. If you can find one on the dealer floor you are better off going that route if you can.
I do not know if you have owned or ridden other bikes other than HD but this is one fine high performance sport touring motorcycle. I do not think you would be disappointed. You may find it difficult to ride with your HD friends. This is no disrespect, but this motorcycle inspires you to ride faster than your HD friends and their bikes might be able to handle.
