There's certainly nothing wrong with taking the bike in to your dealer and getting some feedback. They may have seen/heard it before, and have some insight as to the cause. Should not cost a "fortune' for that, my local dealers would do that for free, yours may not. Can't say.
My only suggestion would be to have a good look at the chain. Clean and lube it,and adjust the tension. Get the bike up on a stand and rotate the rear wheel, see if there's any chain binding or tightness, or hear any odd sounds when you rotate the rear wheel. Might just be the chain touching the swingarm every now and then...
As for the clunky gearshifting and clunky gearbox in general, some have it, some seem not to. The gearshift performance of my 2012 is just fine, better/smoother that some other bikes I've owned. I'm fine with how mine behaves. It does 'clunk' into first gear from neutral. This apparently is a function of the positive neutral finder, or whatever it is that Kawasaki calls it.
It appears that some have had some luck with smoothing out the gearshifting by changing oils. A few threads on that. But with only 1800 miles on it, it's barely broken in - give it some time.
Just my opinion.
Last edited by visitor zero; 06-29-2014 at 10:33 AM.