Wel since you fly out of SFO and I do as well I wil lgive you some roudn about prices. Keep in mind the Yen changes so much and airlines has a new tax on gas..
SFO flight Japan ailrines JAL is about $800
Hotel depends. we stay in Ojiya closer to many breeders.. $350-400 ish
JAL railpass First class about $350
Food depends we are always on the go so we pretty much pick up something at the local market.. I never keep track by I think #150 covers it..
Rental car.. Don;'t even try the international lic. cost to much just ask Mike Snaden
the guide is the broker so you end up paying a percentage..
Joe