If you want cheap flights to Japan you should fly courier. I have travelled to Japan sixteen times as a courier during the past ten years. I returned from my latest courier trip on 7th December 1999. I paid 350 for a return to Tokyo. I stayed for 7 days but you can stay as long as you like.
Prices fluctuate throughout the year.
The hotel in Tokyo is not far from the centre of town and is of good quality - I have stayed there several times. The cost is from 699 depending on departure date. Kyoto is probably the best place to start getting to know Japan. From the very old temples to the very new Kyoto station. It is also very central for Nara, Kobe, Nagoya, also the Akashi Kaikyo bridge the longest of it's type in the world.