tokyo, akabane and yamanashi

Hi! I will be in Japan from October 18 - 25. Please advise if it is wise to travel to these destinations using a JR Pass or should I just pay as I ride (the trains). Please help me also with the right stations to board for these following locations:

October 18
Haneda Airport to Shinagawa

October 19
Akabane (Salesian Sisters' Convent) to Tokyo

October 20
Akabane to Tokyo Disney Sea (chiba)

October 21
Akabane to Nirasaki, Yamanashi

October 22
Nirasaki to Mount Fuji

October 23
Explore Yamanashi

October 24
Nirasaki Yamanashi to Mystays Hotel Haneda

October 25
Mystays Hotel to Haneda International Airport

Thanks!