Checking included or not

Hello,

Here's the trip we would like to do :

3 days in Tokyo
1 stop in Mount Fuji
3 days in Kyoto (with one trip to Nara and Osaka the last day)
2 days in Shiharama (south Osaka)

The bus from Gotambe to Mount Fuji 5th floor is included or not ?
Is there a night route included we can take to go from Shinahara to Tokyo ?