I found flights for around 1100$ during may here Orbitz: Cheap Travel, Flights, Hotels, Vacations, Car Rentals, Cruise, Activities and this site Cheap Airline Tickets, Cheap Flights And Discount Airfares also seems to be helpfull (im from Germany, so im using different sites).

Yeah, thanks. I checked those sites before and I still think those prices are a little high and if I fly out of San Francisco (2 hour drive) from my city then I can get them cheaper. I will most likely end up calling a travel agency who specializes only for Japan travel so I may get a better deal since I read that this is the best way to do it through a travel agent.