Is the shock after your foot comes off the clutch pedal, or happening while you release the pressure on the clutch pedal? Assuming the latter, it usually means you are releasing the clutch too fast, let it out slower. This will let the clutch grab a bit more slowly which will bring the transmission and engine into rotational sync gently. If you just yank your foot off the clutch (worst case), they will be spinning at different speeds, and then there will be a big bang when the two are smacked together.
If you have been driving a manual for a long time and the car just started doing this then it might be a clutch issue. If you just had clutch work done it may have moved the point where the clutch engages up or down along the pedal's throw, and you will need to adjust your pedal release to go slowly over the new engagement point.
Shifting at too low an RPM can make the car jerk as the motor tries to spin back up, but 3000 should be high enough that this isn't the issue.