Japan is perhaps our favourite Asian destination. It is relatively smog free, the food is clean and healthy (no grubs, beetles, spiders etc.) although like most Asian foods it lacks "chew".
We backpacked throughout Japan using the "fast train" network, staying in smallish railway hotels & eating in non lavish restaurants. The rail system is excellent. The trains run frequently and on time - they are also very clean. To get the best price, you must purchase your 7 day rail pass outside the country.
Japan is expensive (avoid taxis at all costs), but it is manageable, provided one exercises care when selecting hotels & restaurants. If you get lost, the locals are very friendly and helpful - they love exercising their English.