1- Newer the better.
2- Cosmetic difference in shape, especially rear lights, and hood.
3- I think you can get the older shape in reasonable condition. I would recommend a good condition older shaped car over a newer one in a bad condition. However, always check the car thoroughly, pay a mechanic/denter to check it for you.
4- Like with any car, exterior condition, signs of touch ups. For interior, look for fading of panels. This car's panels (silver plastic) fade quickly but they are a good indication of how well the owner maintained the car.
5- idsi isn't a very powerful engine and had problems pulling a car on AC with 4,5 people in it. You can imagine what the engine must have gone through in Pakistani summers on CNG with AC. You are smart enough to figure the recommendation here.
6- Depends on your needs. Auto is convenient. Manual is economical to run and cheaper to buy.