I visited Tokyo many years ago and don't remember much, other than that it was January 2-4 and to my surprise the entire city was closed. Went to the big temple, baseball hall of fame, Shinjuku, Shibuya, Roppongi, don't remember where else.
In April I visited Hiroshima and Osaka for a few days and went to Carp and Tigers pre-season games.
Yes, I thought about flying but decided to make use of the rail pass and see a bit of the country. It will be a bit hurried though. Arrive in Sapporo from USA in evening, baseball game at 2 p.m. next day, then 7 hour train ride following morning to Sendai to catch a 5 p.m. baseball game. The rest isn't as rushed.
Then I fly to Bangkok, spend a month in Southeast Asia, then back to Fukuoka, baseball game, train to Yokohama, baseball game,and then fly back to LAX in . . . Singapore Suites, courtesy of Citi sign up bonuses.