I have never owned a bike that changes each time you ride. Sometimes the bike is very low on vibs in the tank, pegs and bars and there are other times when this bikes has much more noise. Throttle response is spot on regardless of this but i can't figure out what causes the excessive vibration at times. The vibs are never in the seat and when you pull in the clutch its smooth as glass so its the motor. Its never to the point that you think there's a problem with the motor just annoying as heck. Amazing how it can go from smooth to buzzy just stopping for gas.
Its done this from when it was new with no mods.
Edit: A buddy of mine just bought a Ninja 1000 and we switched bikes yesterday for awhile, he thought the CB handled great in comparison to the older CB's but asked if its always a bit buzzy, i told him ride it tomorrow and it may be gone

Mine doesn't have any varying feel, as far as I can perceive.
I forget, did you switch out your handlebars and remove the balance weights inside?
Although that would not account for the variable buzziness...
I'm only at 7500 miles, but I am amazed how smooth this bike is every time I ride it, but then I know I don't ride in the rpm ranges that you do either. I'm rarely above 3000 and almost never above 4 and never have been above 5.
Smooth as butter all the time.
I'm with Ferret on the vibe stuff. Smooth as can be. I haven't experienced any perceived vibe issues, tank, bars, pegs - and I ride a lot. And, I've been up in the rpm ranges.
I'm used to v-twins though so I may have built up a tolerance

CIP57, any particular gear or speeds where you experience the annoyances more than others?
(10-07-2014, 10:45 PM)The ferret_imp Wrote: [ -> ]I'm only at 7500 miles, but I am amazed how smooth this bike is every time I ride it, but then I know I don't ride in the rpm ranges that you do either. I'm rarely above 3000 and almost never above 4 and never have been above 5.
Smooth as butter all the time.
I never have time to feel it up in the higher RPM range, there is to much going on there. This is felt with normal riding with shift points between 3500-4000RPMS Above 5000 it tends to flatten out.
(10-07-2014, 11:04 PM)Motogeezer1949_imp Wrote: [ -> ]I'm with Ferret on the vibe stuff. Smooth as can be. I haven't experienced any perceived vibe issues, tank, bars, pegs - and I ride a lot. And, I've been up in the rpm ranges.
I'm used to v-twins though so I may have built up a tolerance 
CIP57, any particular gear or speeds where you experience the annoyances more than others?
Moto,
I feel it the most at about 4000prms ( 70 ) on the highway. Sometimes its smoother than others at this RPM
Being a retired aircraft mechanic I was sometimes tasked with fixing vibrations/"buzzing" at different power settings. Nine times out of ten I would find chaffing conditions in the engine compartment. Check your bike out to assure there is no metal on metal contact anyplace. I have an FJR and installed engine guards with highway pegs, at installation I didn't catch the peg bracket was chaffing some plastic.................at certain speeds I would get a minor buzzing sensation...........repositioning the bracket cleared it.
Cbfan has a point. Now that I think about it on my gen 1 FZ-1 at certain rpms, the inner fairing covers would vibrate against the outer fairing and that could be felt thru the bars. The fix was a piece of sticky backed foam wedged between the inner and out fairings. Buzz gone.
Have you tried it without your windshield?
I've found mine to be very vibey most of the time, to be honest. When I first bought the bike last year, I had planned on putting a LOT of miles on it.. but I'm just taking it in this morning for the 8k service (they threw in a prepaid maint plan, 2 years unlimited miles, everything covered but tires and brake pads).
Unfortunately, my hands go completely numb in about 45 minutes on the backroads or highway, or in about 20 minutes with city riding. It doesn't seem to come through the tank or pegs much, just the bars. I've tried re-positioning the bars, making sure the dampers and bars were set up properly, and new bar end weights - none have helped much.
I actually bought a N1k about 2 months ago as well, spectacular bike but a bit too much to trust myself with on my daily commute. I work nights, and the stock lights were absolutely terrible. Even replaced, it's way too easy to ride too fast for them.
One of the common complaints about the Ninja 1000 is that they are vibey. Strange that it doesn't bother you but the CB does.