I got a 1999 civic hatchback with an b16a swap. When I drive the car just starts jerking. Something like 2 step but while driving. Also one other thing I replaced my intake manifold wit an obd0 engine the plugs are the same. So I just used that. Let me know if that is the problem

 

How are the spark plugs ? I had a civic that jerked like crazy and i changed the spark plug and it went away lol.

 

As HALFKOREANBOY said, check your plugs for any wear. That might cause misfires.

Does the car jerk at a certain rpm if so check your tps since it might have a dead spot. This usually cause jerking at a certain rpm no matter what gear you are in. If this is the case and you have a multimeter you can check your tps for a dead spot.

 

Ignition and timing are my suggestions.
Check FAQ (Look at my sig) and you will find guides for checking both of those.