Interesting. My bike has that jerking stutter at lows rpms. Typically in slow speed traffic I feel it the most. I also notice a slight power surge between 3.5-4k. Once in higher gears and revs everything smooths out. Throttle response has been perfect and as expected, since I got the bike, when it was in worse shape.
When I first got the bike it was really bad. Idle also varied between 900-1500(!), along with low level backfire. I had the carbs rebuilt and it smooth the idle and stutter out, but didn't eliminate it. My mech found a bad coil, replaced it, made the stutter smoother but still there. He pulled out and readjusted things in the carbs, and now the idle is constant, and the stutter is at an absolute minimum, but still there. Still have the power surge between 3.5-4k. Still has occasional low-lever backfire, especially when starting the bike from cold. Pilots are set 3.5 turns out, which is what the fellow China Greg here said was listed in his Haynes manual. I just ordered the Haynes manual, but I don't see this 3.5 turn listing he said is in his. All I see it "Pre-Set" for U.S. models, so I'm not sure where he got this info from and if this is a correct setting. My mech thinks it's way too much. We'll see.
So here's my hunch on this. My bike for some reason does not have a throttle position sensor. My mech checks his charts, and strangely for my 2000 year model the charts do not list one, but it does for 1999 and 2001 models. The cable that hooks up to a TPS is on my bike. I have a feeling my bike needs a TPS, even though it's not listed in the specs. Granted, this is all speculation on my part, but I think that's what's causing the problem.
So, A) does your bike have a TPS and B) do you know if it's working/adjusted correctly? Just throwing that out there.