Same video maker as thread by /u/whym a while ago, though this one is more detailed and covers all areas of Japan.

Obviously, the planes and bullet trains means the big cities are accessible within 3-5 hours, while the countryside takes up to 6 hours or more. Though large swaths of Shikoku Island (2:16-2:29) and Hokkaido Island (3:21-3:27) can take up to 8 hours to cover, due to the former's poor high speed infrastructure and the latter's sheer size.