My Honda Civic 1.5 Ferio has a gearbox problem. There's a grinding sound when I put it into "reverse", and it jerks when I put it into "drive". If I slow down to turn, I have to wait for the gears to initiate before pressing the acceleration pedal. If not, the car will jerk.
It is a second hand re-cond car of 10 years, and I bought it last year. My mechanic it is very hard to find a second hand gearboxfor this particular model. The car is still running.
I think what you are saying is that the shifting is harsh and it jerks when the gear engages. It does sound like you have a transmission problem and the best thing is to get someone who knows automatics to take the car out for a run and check it out.
I am not too familiar with this model, but I am sure that if you look around, you would be able to get a complete engine transmission unit second hand for your engine compartment. You will need to look for the guys who do such conversions as they are very familiar with this work. The average mechanic would not have the experience to do such conversion if he has not done it before.