You can try getting the injectors serviced. at 58000km they are almost due for a clean-up.
But most probably the problem seems to be related to CNG installation. I can't really say how, because I don't have any experience of driving on CNG, since I drive on petrol. The only real way of finding out is to temporarily put all electrical connections back to stock and then check if your mileage improves.
Also test the car on the highway to see how much miles you are getting. Drive with a full tank at a speed of 80km/hr in 5th gear for about 50km, top up again and check the mileage.