Train/bus pass and route

Hi,
I'm travelling to Tokyo staying there few days then going to Osaka, from Osaka intending to do day trips to Kyoto Hiroshima etc then from Osaka go to Mt Fuji - fujikawaguchiko then back to Tokyo and fly out of Tokyo.

The plan is as below. Can you please advice best train ticket to use for all places including within Tokyo, and best route and train bus to get between the cities?
Thanks.
.................. Tokyo

Arrive Sunday 17th arvo so
Sunday 17th night (1 night) +
Monday 18th day/night (1 day 2 nights)
Tue 19th day/night (2 days 3 nights)
Wedn 20th day/night (3 days 4 nights)
Thur 21st day/night (4 days 5 nights)

Osaka

Leave Fri 22nd morning arrive Friday morning.
Fri 22nd half day/night (1days 1 nights)
Sat 23rd day/night (2 days 2 nights)
Sunday 24th day/night (3 days 3 nights)
Monday 25th day/night (4 days 4nights)

Mt Fuji

Leave Osaka Tue morning 26th to mt Fuji
Tue 26th half day night 1 (day night)
Leave Wedn 27th to Tokyo

Tokyo
Half day Wed 27th day/night (1day 1night)
Thur 28th day/night (2days 2nights)

Fri 29th leave to Bangkok