Traveling about 4 weeks through Japan

Hello,
what kind of travel pass should i by while beeing around 4 weeks in Japan?
i will arrive next week on monday in tokio. Staying there for 1 week and then travel to the south. mostly staying acouple of days at one place. inbetween will i fly to okinawa for a couple of days from osaka and back to it again. aftwerwards traveling to fukuoka with a couple of stops and taking there the ferry to Busan.
should i buy in tokio a "city" ticket for 7 days and use afterwards the 21 days JR passs?
what would you guy recommand?

Thanks for your Help
Regars
Philipp