Two suggestions:
When you adjusted the valves, are you certain you used the METRIC measurements on the feeler gauge? Most feeler gauges available in the US have both the metric and SAE measurements on the blade (and some have only the SAE measurements.)
The numbers on top are fractions of an inch, the lower numbers are the fractions of a millimeter--the one you should be using.
No offense intended if you're certain you have the valve clearances set to the metric measurements. It's more common than you might think.
And if you'd like to quiet down the engine's natural, perceived mechanical noise from the rider's perspective, you can always order the sheet foam from another Ninja model like I did. Pictured is the foam set from a 2002 ZX9R I put on my 500's fairing. (Also got the foil/foam sheeting lining the underside of the gas tank, for good measure:
It always twisted my sack that KHI saw fit to put this noise-damping material on their smoother, quieter I-4 engines, but they don't do it on our 500.
Good luck and let us know how it turns out.
Peace!
-CCinC