imtishal, I had the same problem with my civic 96 exi on petrol. I got everything checked including throttle body, tappets etc but the problem stayed. coincidently, the next day my car's battery died so I replace it with a new one and to my surprise the problem was rectified. What actually happened was the micro controller settings got disturbed somehow, which in turn was resulting in unexpected fuel pump behaviour. So removing the battery reset CPU settings to original. As a result the problem was rectified.
You see sometimes the solution could be as simple as tightening a bolt. If you haven't tried getting your car's micro controller reset, try doing that. You can easily get it done by any Honda dealer. Alternatively, a desi way is to completely disconnect the battery, let it stay for 5 minutes or so and then reconnect.
Hope it helps.
