1997 honda civic 5 speed 1 and 2 shift jerks 3/4/5 shift runs great why?

very possible a bad plug or plug wire. In first or second gear there is a greater load and higher rpms on engine which will cause any weaknesses in the ignition to show up.

Check for weak/broken motor mounts, engine generates more torque in first and second gear as there is actually less load on it so torque is greater! If it were an ignition problem it would be more pronounced in the higher gears as load increases but torque decreases. Torque = power which you have more of in low gear. Load = less power try to take off in high gear, cant do it.