When any engine is designed, it is always classified according to various methods. For example classification of the engine according to the cylinder arrangement, valve arrangement, fuel system, compression ratio, octane rating and many more. To cut the story short the engines of modern cars are designed according to the compression ratio which falls between 8:1 to 9.5:1. This ratio call for the fuel of octane rating between 87 to 91. At this octane rating the combustion temperature is approximately around 1292^F. On CNG the engine runs lean with the power loss of about 15-20% and the combustion temperature rises beyond 1800^F for which this engine is not designed. At this temperature the valves do not withstand and start getting inside the valve seats thus partially keeping the valves open. This state gives rise to weak cylinder compression which in turn affects the fuel consumption, start ability misfire and more problems.
To my opinion it is better to replace both the cylinder and head assembly with a good known one of the same configuration. In this way you could get the best results and could enjoy you car for a longer period of time. GOOD LUCK.