The only time I ever experienced what you are describing (as long as there wasn’t an issue with the motor) would be when I downshifted too far (should’ve stayed in 3rd rather than go to 2nd) and I would be too high in the RPM range and any little throttle input would feel like a jerk until I shifted up (or I was too high in the RPM and hit the rev limiter).
What were the RPM’s like when you felt this? If you don’t think it is your driving may I suggest asking someone at the track who drives a shifter to take some laps in your kart to make sure it is running right.
Something that might give you an indicator if the motor is running okay is while on the stand (after warming it up to operating temp) pull the throttle to get around 7000-8000 RPMs, hold for a brief moment, and then yank the throttle and see if there is any hesitation getting to max RPMs (should max somewhere in the 14000 range). All this is meant to tell you is without a load, can the motor rev up without issue given the current setup/conditions. If there is hesitation at any point (after the inital delay from yanking on the throttle) than it’s time to start looking into the potential problems.
To follow this up under load is while on the track (pick 3rd or 4th gear), get the RPMs about 7000 and punch the throttle. The motor should bog and about 8500 it should launch to about 12500 before it loses power. Repeat this (same gear at the same point on the track) but start at 8500 and it should immediately launch to around 12500 before the power drops off.
This is assuming you are running a Honda stock moto…
As Juan mentioned, these things are brutal!!! (but ohhhhhh so much fun) :)