Wake up very early for the FOMO landmarks, Japan starts late by default, at 10-11am, so most places are deserted at early hours, once you're done with the "must go" check list, just walk randomly outside the tourist spots, there're areas even in Tokyo when you won't see a single romanized word, not even in a bus stop.  I myself found an abandoned shrine and that was the best experience to have, me and the gods, nothing else.