Don't know if it has been mentioned, but the search function is not working (it's literally not working, as opposed to not finding anything). Have y'all seen this place:
www.shinsho-an.com in Kyoto? I had dinner at their restaurant, and it was amazing. The hotel itself has 4 rooms, reservations by introduction only, and rates start at JPY 170,000 per night for two. On the upside, the rate includes breakfast in the room and dinner for two in said restaurant (where dinner will set you back no less than JPY 40,000 for one).