WA 
1- Both ways (KKH and Kaghan Valley) take almost same time. But KKH is very hot and nothing much to see around while Kaghan Valley weather is superb with so many attractions on the route. Both routes join at Chilas.
From Mansehra it will take around 12-14 hours till Chilas while 10-12 hours through Kaghan Valley if u don't stop anywhere. But definitely there are so many locations on the way like Kiwai, Kaghan, Naran, Batakundi, Jalkhad, Lulusar Lake, Babusar Top so its hard to ignore all of them So at the end u spend same time reaching Chilas but Kaghan Valley route is highly recommended in September.
You can make it in one day if u start from Lahore at midnight and reach Mansehra early morning.
2- Robberies happened in June 3rd week but no such news after that. It is safe to travel in day time as Asif said. Lately, army was working on Nuri Top road so it should be open in a week or so. If u want to visit Nuri Top then i would recommend to stay at Jalkhad and then on 2nd day reach Fairy Meadows directly through Babusar pass and Chilas route.
3- It will take 1hr-1.5 hrs till Raikot bridge from Chilas. Hotel rates are in the range of 1000-2000 per night. Food is not good at all and unreasonably expensive. In short, not a good place to stay unless u r breaking journey at night. You should visit Nuri Top on day one and stay in good weather at Jalkhad.
4- Way to Shogran starts from Kiwai on Kaghan Valley road which is hardly an hour drive away from Balakot. Chilas is nowhere near this place.
5- No issues at all in September. All ways will be open specially high altitude passes. Rainy season would be over but at same time greenery would also be less. It will be chilly cold at night at Fairy Meadows so take warm clothes. The height of Fairy Meadows is just around 10,000 ft but it faces a huge mass of ice rock in shape of Nanga Parbat and bone-penetrating chilly winds blow down the valley all the time so be prepared for that.
The climate change from Raikot bridge (35-40 degrees) to Fairy Meadows is quite sudden so don't expose sweating body to cold or u will get cramps etc.
