I also own a Civic EXI M/T December 2005, converted to CNG. My experience has been extremely good so far. I think it depends on quality of CNG fitting or may be just the settings are out.
Anyways, my experience is that it should give around 100 km on A/c adn 110 (or maybe slightly more) without A/c in Lahore. On motorways, I touched 157 with A/c last time. So, I guess there is something wrong with the settings. Besides, the jerks and missing should not be there at all. Yes, the pick would reduce, but it will still be a very good smooth drive, as in my case.
Have it checked! I can recommend you to a very good person in lahore. For CNG setting, this man is excellent... my personal experience. There is a PSO petrol pump on your left when you are going from Kalma Chowk towards PU New campus, just after the barkat market signal. The guy's name is Abid and the name of the workshop is Enercon. He sits in a smallish room just next of PSO pump. There is a Shell petrol pump as well, right next to the PSO.
I am certain your problems will be solved! Do keep me posted....