WAS, Dear Asim,
Nice talking to you. As far as the mileage is concerned, I do want to mention that I have removed the entire CNG setup from my car to bring it to factory setting and get optimum mileage and performance on petrol. That includes removal of specifically CNG injector nozzle(putting a kabli unaltered throttle-body) and the cng cylinder + allied electronics. Secondly, the engine burns lean on CNG causing damage to valves. As per your saying that you have recently overhauled the engine, let it run for atleast 1500 km to properly break-in and it should gradually come to the desired performance and economy.
I hope Tahir must have checked everything and made replacements where necessary(as discussed with him on phone).