I think that we are talking about varying degrees of misfire here. What Raven is describing is known as "lean surging" and happens with many bikes in stock form. I know that my '05 does this until I installed a PCIII. My idle is still not completely rock steady, but the surging at lower rpms with small throttle openings is completely gone.
I think
probably that the OP's condition is worse and different, more acute, since he says that it didn't do it before a certain point in time. Of course it could also just be that he has become more aware of the sensation and is therefore now looking for it.
That was the thing for me. Before my FJR, I had experienced lean surging on both a '94 BMW R1100RS (fixed w/ a Techlusion EFI box) which surged pretty badly on the early Fuel Injection mapping and with a 2001 Concours (fixed with larger pilot jets), so I am all too sensitive to it.
The way that I describe the feeling is that it's like you are always bucking a gusty headwind, but only when cruising at a constant throttle. Then as soon as crack the throttle open and give it some gas it gets much smoother.
I know of people that ride bikes that surge all of the time, but because they are not sensitive to it, it just doesn't bother them. This was true even of the BMW oilhead crowd, where a good portion of owners were in denial about the rudimentary first generation FI maps. Amazingly, when BMW came out with more complex FI systems and dual spark plug heads the surging went away...
edit - Forgot to mention that My V-strom also had the lean surging until I installed a PCIII on that too. Other people use a Yosh box to reprogram their ECU fuel injection maps.
The only bike I've owned recently that has never surged is my 1998 VFR800Fi. It was the first year of fuel injection for the Interceptors and is a bit different in that it is an open loop FI system. There are no Catalytic convertors, and so therefore, no oxygen sensors. Coincidence? I think not.
That is one smooth running engine. I believe they messed it up and added the cats and O2 sensor in 2000.