Nakano is one of 23 wards in Tokyo, the capital city of Japan. This is the location of Kafka's (and Johnnie Walker's) home, and it is also the neighborhood where Nakata resides.
Kobe is located further south on the main island of Japan (Honshuu), and it is the 5th largest city in Japan. This is where Hoshino stops to deliver his last trucking delivery before taking leave from his job to help Nakata get to Shikoku.
Shikoku is a small island, south of the main island, Honshuu. There are three large bridges that cross from Honshuu to Shikoku, and Hoshino and Nakata take the Kobe-Awaji-Naruto Expressway to Tokushima.
Tokushima city is the capital of Tokushima prefecture, located in the north east corner of Shikoku. Hoshino and Nakata take the train from Tokushima to Takamatsu.
Takamatsu is located in Kagawa prefecture on the north side of Shikoku. This is where Kafka and Nakata find the Komura Memorial Library. It is also where Hoshino and Nakata find the entrance stone.
Kochi is a prefecture on the south side of Shikoku. There are mountains on the north side of Kochi, and this is where Oshima's cabin and the deep forest are located.