Wow, LapLap! Thank you so much!
I've started to breathe again--I was very nervous about the cost but I think it will be okay and I think my mom will love Japan!
I found a flight on United that would get her into KIX but leave from NRT--which would be great. We could visit Osaka/Kyoto for a few days and then go to Tokyo.
I also realized that I don't have to abandon my previous plans. I was going to stay with a friend in Otsu and with a friend for a few days in Tokyo (and dorm the rest). From what you say, it looks like getting a twin doesn't save any money so I could get her a single and stay with friends on the nights that I was planning. I'll give the dorms a miss and stay in a twin with her on the other nights.
Once she gets her ticket (tomorrow, I hope) I can start worrying some more, but thanks so much for this--the map is great!