First you should Check out your Transmission oil level that could cause your car too jerk into gear. The only other thing it might be if the transmission is going bad and you should have it checked by a transmission specialist
I am not a mechanic but I do own a 2000 CR-V on which I do a little of my own work. From your description it isn't clear just what might be causing the 'jerky' feeling but before you consider the transmission, I would recommend having your motor mounts checked. A broken motor mount could be a possible cause the jerky movement you are experiencing. If it is not a bad motor mount then I'm sorry to tell you that you might be looking at some transmission work. Just how expensive that might be can only be determined by a competent repair shop. There is no "home" remedy that will solve a transmission problem.
A corroded distributor cap and rotor will cause a vehicle to be difficult if not impossible to start and may cause the motor to run rough. If a manual transmission is jerky the clutch slave cylinder or clutch may need replacing ( clutch slipping ). It would also do to check the clutch lines for leaking fluid.
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