The Price seems OK, in Karachi that car can be purchased for 1.5M though.
Do not worry about CNG, AT transmissions have noting to do with CNG, running my Civic PROSMATEC for past 30K km's, no problem at all.
I think more then 50% of post 2006 Civic's and 2008 Corolla's are on CNG, apart from those which are company maintained.
I have also seen CNG in many Auto Premio's and in one Prado.
Just check thoroughly the engine mounts and suspensions for any noise or rattle.
Also please check the CNG conversion by driving the car on CNG, lock the transmission into D3 and floor the accelerator to check the throttle response/engine power and if possible the fuel economy, it should not be less then 70 Km in a 55 kg cylinder in whatsoever driving conditions (other then a traffic jam), 105-115 on Highway (with A/c).