JAPAN
Infos about the trip

In Japan you can find very good infrastructures and therefore the organization of a trip don't introduce big difficulties to exception of the linguistic barrier that sometimes can make complicated some situations.

ITINERARY

TRANSPORT
For traveling inside the country I used almost exclusively the trains, the only definition I can give is: a perfect service. 
The only negative side is the high cost of the tickets, for this, if you plan many moves it is absolutely useful the Japan Rail Pass, only the foreigners can buy it and only outside Japan, gives the possibility to use almost all trains, a lot of metropolitan lines and also some ferry's.
Even the city transports are efficient, a morning in Tokyo the doors of the train didn't open immediately, the conductor was stopped 1 meter over the expectation and he returned back and to that point the doors opened. 
To the exception of Tokyo all the signs in the trains and in the stations are only almost always in japanese.

WEATHER
During my trip I found quite cold weather but with beautiful days.

FOOD
Before the departure many people told me that the food is not so good, for me instead was quite good even if after a little bit the tastes seem all equal. 
The basic dish is constituted by soba noodle: buckwheat noodles, are usually eaten in broth with vegetables, fish or meat; I liked a lot the cold version with seaweed and soy sauce. 
Absolutely to try the sushi: raw fish (fresh) with a bed of rice; 2 types of sushi restaurants exist: those classical where the customer chooses the piece of sushi and the cook prepares it and the kaiten-zushis (less expensive than the first ones) where the dishes flow on a blest and the customer choose what they wants. 
All the dishes are generally accompanied by green tea.

Dangers & annoyances 
I can only say that is considered the safest country in the world with a very respectful society.

Costs 
Japan is also an a little tourist destination above all because is considered a very expensive country, to me the costs are not seemed prohibitive, in general no more than 10-15% in comparison to Italy (considering the good exchange rate in the period of my trip).
Japanese uses almost exclusively cash, in all the averages and big cities ATM are found for the withdrawal of cash even if is necessary to choose those with international cards.
Average Costs (1€ ~ 132 ¥):
light lunch or dinner in a restaurant= 1000 ¥
McDonald's menù= 540 ¥
bed in a hostel/guest house= 2200 ¥
city trip with bus/subway= 200 ¥
visit: monuments, temples and museum= 350 ¥

Lodgings
I lodged in hostels and pensions. 
Almost all the lodgings have laundry service, for the costs and logistic difficulties the lodgings for the backpackers are almost always fully booked therefore it is worth to book in advance. 
The pensions where I stayed:

Kyoto
Budget Inn: 10 minutes of walk from the central station, the personnel is very friendly even if very fiscal, the rooms are quite cold because the owners want to contribute to the reduction of the harmful issues; dormitory, 2400 ¥.

Hiroshima
Mikawa Ryokan, tel. 261-2719: small but quite pleasant, to feel the experience of the ryokan, the owners speak only japanese; single room with common services 3400 ¥.