City comes with CVT Continuous Variable Transmission, that varies the gear ratios according to various parameters. Now if the entire fuel system is changed, that means, atleast 10% difference in the power while car running on CNG, CVT is be calculating the gear ratio accroding to Petrol, while engine is running with 10% power stealing, hence one may feel a total lack of power during driving, but it shouldn't affect the gear box...!
If you really want to improve the performance, you need to install constant feedback CNG system (Lambda Emulator) alongwith Advancer and Injector Emulator[although you should have the later two already installed], that will decrease the 10% margin to almost 5%, and you will feel the drive much better!
If you want to remove CNG, nothing has to be changed, just remove the CNG Ventury, the Regulator, the Cylinder and the switch. If advancer is installed, you have to resume the connection interrupted by the advancer!