I've got no idea how's the situation of CNG these days, but about your travelling you have got 3 routes available:
1. N55 all the way till Hyederabad and then M9 to Karachi. The longest of the 3, and relatively riskier amongst the 3 as well. Although you have multiple options to connect either to M5 at Multan, or N5 at various other cities. My guess is that this will answer your concern about CNG but be mindful of the days on which CNG is not available.
2. N55 to Multan via Kot Addu, then M5 to Sukkur and then N5 to Hyderabad, and then M9 to Karachi. A mix of both CNG and petrol as well as highways and motorwarys will do the trick for you. Please remembers that there are hardly any fuel stations on nearly 400km stretch of M5 from Multan to Sukkur. So you either have to refill the tank at Multan or leave motorway at any exit, refill the tank, and reconnect to M5. Toll is not an issue by doing this as it is calculated on per km basis.
3. M1 to Islamabad, M2 to Pindi Bhattian, M4 to Multan, M5 to Sukkur, N5 to Hyderabad, and then M9 to Karachi. The most enjoyable and comfortable route of the 3. Kindly ask other members about the availability of CNG on these motorways till Sukkur as I guess it's available on N5 at multiple locations.
Regards