First off, 160km/cyl is a bit tooo much for a civic to do. i guess the previous owner lied to u. civic is not a car that is good at fuel economy. even the manual ones are heavy on fuel. many of the civics that i have in family and friends do no more then 110-125km in local driving conditions and upto 150 max on long drives. but 60km is still way too less. all u need to do is to get everything checked. get new air filter if its clogged. check if theres too much oil on the cng kit , u need to get the kit serviced. whats the condition of plugs? tappets adjusted or not? throttle body service done or not? these are one of the few things that can affect mileage of a car. after all the service, get cng tuning done from a well reputed mechanic.
as for the hot air from the vents, is it PROPERLY hot as if the heater is turned on to full or is it just not cold as u wud expect it to be? if its really hot then the problem is with the motor or the valve that xulfiqar bhai mentioned. if its just not cool enough, then its normal. on fresh air inlet opening, the air that comes in is usually hotter then the normal air temp outside as its passes very near to the engine and picks up some heat.
to check the valve/motor etc, turn ur a/c fan on and (when the car is hot) turn the heat knob to full red position, see if the air gets even more hot or not, if it does then the motor is working fine if it doesnt change the temprature then the motor is probably dead or may be some connection is loose...