I have an 05 that i bought new in 05, it has always been that way, never had a problem, only at low speeds and mostly first gear do i ever even notice, as a matter of fact I think it was only when I was getting used to it. I think I shift at different times now, I have gotten familiar with that little Quirk and made a mental adjustment to my downshift points etc. I think I just got used to it more. I think these bikes are designed for high revs, they run soooooo smooth at 11-12 k rpm, I think that the same thing that clunks is the same thing that acts like a shift kit and propels you forward at 12k rpm's. Well, maybe it is because I speed shift, luckily it has a rev limiter and I have only missed a gear once.I do ride pretty hard and no issues at all with it.
An 05 with 800 miles, mmm yummy, how much$ I like the 05, I looked at the new ones every year and did not think they were as pretty as the aluminum frame of the 05. Also some 07 models and up only have 76 hp like the FZ6R.
I think unless you get the S2 model. Don't quote me though, some of the tards at the bike shop give wrong info sometimes.You would think they would know their craft better or go work in a car lot. Anyway, I ramble.
I must say that the Fz6 is a rare creature when it comes to bikes, I don't know of anyone who has ever been disappointed after getting one.