Bro,...i had almost the same problem,..with a difference that the situation worsened in the end,... the heavy sound changed into "complete timing out".
Is ur problem both on CNG and Petrol or on just CNG ?....
Mine was with both CNG and Petrol, Car was under powered, didnt go beyond 80 Km/hr, and mileage was just ok, not superb!... but Alhamdulillah after rectification its rocking! (even the mileage has improved)
My mechanic did a step wise diagnosis....These are my recommendations:-
1) Get the tappets checked (only get them adjusted, dont change them cuz thts wot mechanic may recommend 
)
2) He checked the car for timing error (he opened the side cover beside the engine to check it "thats where the timing belt and different gears are accessed, sorry cant tell u with exact terms, but he checked whether THAT gear which is responsible for ply but in my case it was ok" )
3) Last but not the least, my problem was that my GASKIT was damaged (n i suspect thats the same case with ur car) ...method for checking this without opening head is , check whether the current is coming in each plug, and den check the change of sound removing plug one by one) This will tell u whether all the cylinders are working or not..
My fault was detected cuz number 2 and number 3 cylinders were not working "no compression",...mechanic said that ur valves need to be changed , but when he opened the head, the culprit was the GASKIT. Remember that its not necessary that Santro heats up when GASKIT is damaged. And even my car's GASIT was damaged it didnt boiled the radiator water, or it didnt heat up the car.
My GASKIT was changed (it costs Rs 350/ Genuine) and my car Mashallah is flying .... :).... Hope it helps ...
I suspect that if its not sensor problem than ur GASKIT is the problem.
AND feel free to pvt msg for any details 
