I was in Japan a few weeks ago. No injections needed. Everywhere is clean. Everyone is friendly. Crime is relatively low. If she's planning on travelling round I'd highly recommend the Japan Rail Pass. It's great value and unlimited travel on Japanese Rail trains. You can get from Kansai airport to Osaka and Kyoto and use it to travel hundreds of miles across the country to places like Tokyo. And even ride the bullet train.
Kyoto is stunning. Lots of temples and highly recommend visiting the bamboo forest.
If she's visiting Tokyo a visit to Mt Fuji is a must. Best view is getting the train to Lake Kawaguchi.
I have lots more Tokyo tips, so if she is going there let me know!