most likely u would need to get the Transmission overhauled.
Auto Transmissions are built well and hence are even more durable and longer lasting than manual transmissions. In majority of the cases, engine wears out well before the transmission needs any work.
The Auto transmission failure is the result of abuse, not changing transmission filter and fluid on time and Improper Alteration.
The Auto Transmissions can handle CNG Kits. The problem occurs when the kit is installed improperly or when the parts are not genuine or if the kit is not for the car.
For example a CNG kit for a corolla is diferent from that of a Honda and incorrect installation would certainly cause problems, accelerated wear and tear and in worse case scenerios, out right failure.