We visited Japan in the mid-00's and outside of Kyoto found a real shortage of latin-lettered signage. Our train and hotels were set up by a friend so we didn't have to deal with that and fortunately there were readable letters with the train and an appreciation of my business cards when checking in. Otherwise, there was a lot of pointing and Indian food involved. Have things changed since then?
Edit: When we were there our GSM phones did not work in Japan - we needed to have a rental. Has the spread of iPhones meant that non-native phones can work in Japan?