Hi there,
I would recommend the following itinerary since in this way, you will need to take a bus only for Kawaguchiko to Kofu, Matsumoto to Takayama, and Takayama to Shirakawago/Shirakawago to Takayama. You can just use Japan Rail Pass (JR Pass) for the rest of routes.
[Day 1]     Narita > Shinjuku > Kawaguchiko 
[Day 2]     AM: Sightseeing Kawaguchiko 
               2 PM: Leave Kawaguchiko > Kofu >Matsumoto
[Day 3]     AM: Matsumoto Castle
               3 PM: Leave Matsumoto Castle >Takayama
[Day 4]    Sightseeing Takayama/Shirakawago
[Day 5]     AM: Leave Takayama > Nagoya > Kyoto or Osaka
[Day 6&7]  Sightseeing Kyoto/Osaka/Nara
[Day 8]     Leave Kyoto or Osaka for Tokyo 
[Day 9]     Tokyo
[Day 10]  Tokyo > Narita Airport