JNK ~
You're lucky to have the chance to actually ride the two bikes. That doesn't happen often enough in this day and age.
I related here a couple of months ago that I had bought a 2006 FJR to add long distance touring capabilities that my old Zephyr 750 didn't have. While I was in the selection process, I looked carefully at the C-14, the Feejer, and the ST-1300 Honda. All are very nice bikes, with varying strong and weak points. Each of us has to figure out what is going to work best for US, then buy to suit that need.
For me, it was the seating position and height of the C-14 that swung the deal to the Feejer. I am inseam challenged, with stubby little 28" legs. Because of the difference (slight) in height, coupled with the slightly less wide seat, the FJR fit me better. I am able to flat-foot the Feej by sliding forward a bit on the seat. Could not do that on the Connie.
I don't know how many miles were on the test bike you rode, but my FJR with 4,000 miles on it shifts like butter. In reading the ton of info over on FJRforum.com, it seems usual that the tranny is a little "clunky" until it gets broken-in a bit.
You seem to really perseverate on the 6-speed tranny... Different strokes, I guess. With approx 140HP on tap, and a torque curve that is remarkably flat, I find the Feej to be acceptable, if not preferable with the 5 speed. It loafs down the slab at 75 - 80 MPH with no noticable buzziness. I've had it a bit north of 120 a couple of times, and didn't note any lack of smoothness at those speeds either. In reading a lot of the posts on this and other boards concerning the C-14, many riders report better fuel mileage while running in 5th gear, saving 6th for runs well above legal speeds on the slab...
My bike has heavy bar end weights installed, so perhaps that helps smooth things out a bit?
I guess it all boils down to what lights YOUR fuse!
We, as riders, are really lucky to have three nice alternatives to consider, eh? Any of the three will serve you well, depending on what's most important to you... Enjoy the search!
Just an aside... your post would be much easier to read if you used capital letters to begin sentences... but you knew that, right?
Let us know how your quest for the bike turns out!
Don