Buddy there is no problem in 99 model Vitz, AC is okay, just read the AC filter cleaning DIY post here on forum for Vitz. It will make a lot of difference, secondly get the gas checked. Lack of acceleration maybe due to throttle body requiring cleaning, bad plugs,air filter. Get them checked.
Secondly, there is absolutely no problem in 99 vitz with CNG, ive driven my friends 99 vitz with 115,000 Km mileage on CNG (it cost him total 32000 rs) and it works accelent, better than any car, just make sure that you get it installed from a good installer. Cheers!