To OP: you live in Kyushu and you are asking your question on this forum? Why not ask on a local Japan based website, like japantoday or some other English based forum in Japan?

Based on my Japan experience (lived and worked there 15 years, but last in Japan about 2 years ago), I would say this:

1. For travel over long distances, go Skinkansen, about Y15,000 Tokyo to Osaka, if I remember correctly.

2. For hotels, perhaps you should stick one major group, medium priced, like the Tokyu group or Keio Plaza group where the nightly rate is maybe 10,000 - 15,000 yen per night. You should also plan a stay or two at a Japanese ryokan or onsen (hot springs), and for better onsens, you're looking at 20,000 - 30,000 yen per person per night, inclusive two meals (dinner and next day breakfast).

3. For daily food, a budget of say 3,000 - 5,000 yen per person per day should be sufficient.

Or you can just go to JTB and have them arrange the whole itinerary for you.

Have a great time with your GF.