12310,

Try to book your accomodation earlier, using booking.com, etc.  For flight use Air Asia/ Mas on offer.  for travel buy train pass for the duration or a payment card.  All these you can pay first by credit card.  We bought JR Pass for 7 days as we travel by Shinkasen to Osaka, Hiroshima, Kyoto, etc.
For Hotel, we stayed at "Shinjuku area in Tokyo, and Shinsabashi in Osaka. Food is not expensive, depending on where you eat.  Breakfast is less than 500 Yen, Dinner is also less than 1000 Yen, and this can be taken by two persons.  Popular family restaurant is Sukiya where the beef rice is less than 400 Yen.  We went twice on our own to Japan, and used this method. Yen now is cheaper as we paid nearly 33                      RM for 1000 Yen. hope this info helps.