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Three weeks to go deep — the classic triangle plus the underrated west coast, an art island, and the southern island of Kyushu.
Build this tripFly HND. Days 1-5 Tokyo: standard hits plus a night in Shimokitazawa and a day in Yokohama. JR Pass covers the train portion. Day 6 shinkansen to Kanazawa 2h30m, 2 days for Kenrokuen garden and the samurai district. Train to Kyoto. Days 8-11 Kyoto, including a morning trip to Nara and one day off the tourist trail in Ohara. Day 12 train + cable car to Koyasan, stay in a temple lodging, attend morning prayers. Day 13 back to Osaka, 2 days Dotonbori and Osaka Castle. Day 15 shinkansen to Okayama, ferry to Naoshima, 2 days for the Chichu Museum and Tadao Ando architecture. Day 17 return, shinkansen Hiroshima, 2 days including Miyajima. Day 19 shinkansen Hakata/Fukuoka, 2 days ramen and relaxation. Fly FUK home. Use the 21-day JR Pass.
March-May (cherry blossom) or October-November (fall colors).