What is your plan of action after uninstalling CNG Kit, because I can help with your CNG issues. My Alto K10 was installed with Tomasetto Sequential kit and faced same kind of issues. Finally all the major issues were resolved.
1. The most important thing is clean up the Throttle body. This would resolve 70% of all CNG issues. May be Honda people will say the Throttle body is very fine with petrol but still you ask them to do it.
2. Reduce the Spark plugs gap to 0.7mm ( Better to find how much gap the Honda people suggest as they have release CNG version in Honda City).
3. May be people say 'Timing advanser' is not required for Sequential kit but I say it is required. This will make your car more stable and increase pick up.
4. As CNG comes with high pressure from tank, all the pipes must be clamped at every end.
5. While the installation is in process, sit with mechanic and observe any warnings are displayed which are been ignoring. This is very important because all injectors must be perfectly configured.
Let me know for any other issues, because I was gone through most of the issues which you had faced