First go for Ultra-sonic Injector cleaning. Must be available in good workshops. In Islamabad and Lahore it costs around one or two thousand ruppees for the injectors cleaning (upto 4 injectors). If it does not work then go for other expensive measures, like changing the injectors.
Note: i am also having the same issue. My car's RPM sometimes gets uneven on petrol, and car turns off on its on. whereas on CNG it remains perfectly okay. (and there is no check engine light. So the Throttle Position sensor is correct.)
things i did so far in the last 3 weeks:
1) Throttle body cleanup with carborator cleaner spray (Rs 200)
2) changed fuel filter (Rs. 650)
3) Cleaned the sieve (small gauze attached to one end of fuel pump, labour Rs.500)
4) Ultra-sonic injectors cleaning (Rs. 1000). The injectors are working 100% correct.
The problem however, sometimes occurs again, despite doing the above. Next target is:
5) Fuel pump assembly (which is gonna cost close to 6 to 8 thousand ruppees, as per the auto-parts store, big expense)
.....
Suggestions are welcome.