If you are thinking to travel to mustang from Pokhara/ Kathmandu. You can take chartered helicopter flights right out of Kathmandu. But the preferred route is to get to Pokhara and fly or trek from there. There are air and ground transportation to Pokhara from Kathmandu. Then you could fly from Pokhara to Jomsom and from Jomsom trek to Muktinath. You could also use the Jomsom Trek route from Naya Pul and trek to Muktinath which takes around 8 days.
Alternatively, try the Annapurna Circuit route from Besisahar (Lamjung) and trek to Muktinath which takes around 10 days.
A favorite way these days, is this route. Â Drive from Pokhara to Beni on a day or night bus which takes around 5 hours. From Beni, take a jeep to Muktinath which takes the whole day. You need to change the jeep in Jomsom as the bridge in Jomsom is not completed.