Transmissions: For street use most transmissions give good service without modification. They vary in design but most have five or six speeds and operate by rotating a shift drum with cam slots that move shift forks which in turn slide the gears back and forth on the shafts engaging and disengaging the gears. The gears are mounted alternately on the shaft in either a splined or freely rotating condition. Adjacent gears have engaging dogs or slots that lock together when moved into contact with each other. When locked together a pair of gears is then able to transmit power from one shaft to the other at a particular ratio.
A common failure mode for this type of transmission is when the locking dogs fail to stay engaged. Symptoms usually involve jumping out of gear or chattering when power is applied. This will typically occur in only one or two gears initially. If left uncorrected the gears, shift forks, and shift drum may be damaged. A good transmission will have all the engaging dogs undercut on both the upshift and downshift sides and the gears shimmed to avoid thrust loading the shift forks. These modifications provide for positive gear engagement and minimal power loss through the transmission. Many stock transmissions have no undercutting or shimming, some have one or more gears done, almost none have all gears modified.
Zlock Racing has transmission modification services available for selected models. The 98-99 ZX9R is a common example as it had a nasty habit of jumping out of gear. Your particular needs are best addressed as an individual case based on model, performance, intended use, and cost. If you think transmission work is needed we would be happy to discuss the specifics of your engine.