Travel within Japan Options

Hi there, 4 adults travelling to Japan in March/April.
We will arrive Haneda airport from Melbourne and stay in Tokyo for 5 nights
Tokyo to Mt Fuji - 3 nights
Mt Fuji - Kyoto - 3 nights
Kyoto - Osaka - 2 nights
Fly out of Osaka to Vietnam

Could you please provide best option for travel to these places as not quite sure what would be most economical.
Thanks for your help.

Julie