I once went to Japan during an unusually hot and muggy September, and my feet began to swell in the heat, making walking really painful. Unfortunately, my feet are U.S. women's size 10 (which I believe is 40 in Continental European sizes), and the average shoe store in Japan just doesn't carry anything that large.
However, as I was limping through a station arcade one day, I saw that the adjacent department store was having a clearance sale on European-made sandals. Unlike the U.S., where the large sizes sell out first, the large sizes were left over! I managed to find a comfortable pair of dressy sandals, for which my feet were extremely grateful.
I'm not aware of any shoe stores in NRT. Your best bet for finding shoes in Japan would be a department store that featured European imports.