I disagree with the majority on this one. I have a '00, just broken in, at 1.1k miles. I find the "engine" smoothness to be noticeably deficient in two ways. At slight throttle, light load, at slow riding speed independent of gear selection, the engine stumbles, or what others claim feels like
"surges". This condition may become even more pronounced after installing an aftermarket exhaust, definitely the case on my Busa.
The other area where the Busa lacks in smoothness, (which I read in some of the magazine reports on the '99), is at around 4700 rpm the engine. At that engine speed,
in any gear, you will find there is a noticeable vibration or a so-called "rough spot". I think this is characteristic of all the Busa, whether '99 or not. My '00 certain has it and definitely noticeable, but not really a problem or of any genuine concern.
The slow speed stumble IS, however, very bad and I am currently looking for a solution . . . PC-II?