If I were you I'd get myself a '08 1.0L. The top-of-the-line Vitz varient is called the 'ILL' package it comes with a 1.3L 2NZ-FE 85HP engine, an RPM meter, 2-way climate control system, button start ignition system, smart key, keyless hatch operation, Beige interior, Beige leather seats, optional Tv/Navigation, optional backup camera, optional alloy rims etc.
Both of them are also same when it comes to economy and both of them are identically the same when it comes to comfort. The '06 and the '08 are pretty much the same with only a slight difference in the exterior such as the front and rear bumpers, front and rear tail lights, interior cloth pattern, speedometer cluster color.
As far as the engines are concerned the 1.0L 1KR-FE is around 70HP whereas the 1.3L 2NZ-FE is 85HP and the 2SZ-FE is 85HP.
P.S: If you can afford a car that cost 1 million+ PKR I think you can afford it's fuel aswell, installing a CNG kit to a vehicle with a CVT transmission is not advisable at ALL.