I spent 3 months in Japan, just in Philippines atm and going to Thailand in a few days. I did Japan first as I love it, was my first time and I will go back again (with a JR rail pass next time). It is really easy to eat affordably, just find a great sushi train only 100 yen a plate some of them, or a ramen with some gyoza will only set you back 600-800 yen and you will be full. Most people I know end up spending double their food budget on alcohol so look for places that offer Nomihodai (all you can drink 60-120 minutes) with your meal or at a karaoke place.

Transport is a pain if you are trying to swap cities it is expensive. I took that Willer 123 bus from Fukuoka to Osaka and it was pretty good except the seats are not designed for my size, even deluxe was a squeeze but still a much better experience then all the PI buses I have ridden these last few weeks.

The website Japan-guide.com is great for general info and what to see and also info on travel passes. All day bus or subway passes are great if you plan ahead. For example there is a pass that gets you 3 days (non-concurrent) to go from Osaka airport and encompasses the whole area of Himeji, Nara, Kyoto, etc. You can use it one day in Osaka and end up in Kyoto, then spend the next day using the unlimited Kyoto bus pass for 500 yen, then use your pass again to get to Nara and somewhere else, then final day to get back to Osaka airport or whatever.

There are also special passes for return to Kamakura and also a Nikko train pass from Asakusa in Tokyo that I used that includes unlimited train and bus use for a few days in Nikko area, excellent value.

I also had a Northern Kyushu pass which let me travel for 3 days in a row for 7000 yen with some people who had JR shink passes. As there are no shinks in Kyushu they had to take rapid express like me and I went from Nagasaki (great place) to Mt Aso volcano, then Beppu spa town, then Fukuoka, dropped my bags and went to Sasebo for a few hamburgers then caught the train back to Fukuoka 2 hours later. Good times.

In terms of accomodation, I mostly stayed at hostels as I am only 30. Book on Hostelworld or hostelz.com. The rumours of expensive Japan scare away a lot of your 18-20 year old crowd who would rather party in SE Asia, so the quality of person at a hostel in Japan is totally different from what you will find in Australia, Thailand, India. Everyone is more mature at least 22 and the median would be about 26.

Tokyo - Khaosan Tokyo Annex, Smile and Samurai all in Asakusa nice area near a temple for 2000 a night or 2500 for a capsule for a little more privacy (Annex only). I stayed like 5 weeks at Annex, crazy but awesome fun. They have a Khaosan bar down the road.

Tokyo - Aizuya Inn is sort of same general area near Asakusa out of 'central' Tokyo but easy to train around. Stayed here to recharge my batteries because they have private tatami rooms and superfast wifi. Have to pay 100 yen for the time shower though but very up-market hostel. Lots of french around for some reason.

Osaka - there is an area called Dobutsuen-mae which has a bunch of cheap private rooms. I stayed for a long time at Hotel Raizan, they are about 2100 a night with a public bath and a private shower, shared bathroom but you get a nice room with good Air-con, single western bed and TV and fridge. Very nice for the price. The area is 'dodgy' for Japanese people but I would rather spend a lifetime there then 5 minutes in Manila. Really safe just old out of work guys walking around. Only 20 minute drunk walk back from Namba.

Kyoto - Spent 3 nights at Hana Hostel, really close to JR station, real quality bunks, part of J-Hoppers chain but a 'hybrid' hotel/hostel so had a nice feel. Did Nara day trip from there.

Nikko - Minshuku Narusawa Lodge great lady picked me up from station in rain and brought my bag to station day after, bit out of town but I walked it easy enough. Was a proper minshuku with huge private room and affordable.

Would not recommend Khaosan Fukuoka or J-Hoppers Osaka, better options around.

by the way I hear that Himeji castle is under renovation for the next 4 years LOL, so you can't see it it is covered up and you definitely can't go inside, so I skipped it. There is so much to see in Kyoto you would need 3 days there and another in Nara so don't bother with Himeji.

Anyone reading this can PM me if you have any questions I am happy to help.