Nothing special at all about this price, I don't know why you think it's a deal?
If you're planning on using a rail pass research Japanese public holidays and definitely avoid Golden Week. I usually travel in June->July, weather great, no typhoons and empty green cars on the trains. OK price but I've never paid more than £405.
I travelled this year. Used Expedia.jp from Amsterdam to Tokyo for £190-00. Luton to AMS cost £14-00 each way with squeezyjet. Found it on Holidaypirates
I have to go during the summer hols (and i go every year) but i always manage to get a flight for less than 700 quid even then. You just need to keep searching every day to catch the very limited special deals. This year it was Air France and last year KLM, before that ANA and before that Qatar Airways. KLM were fine and would fly with them again.
I always thought that but this year my mum, who goes to Mojacar a few times a year, only paid £123 for return flights booked 4 days before she left and with 2 separate airlines (Thomas Cook there, Monarch back). I usually find her flights because she always spends close to £300 but this year (twice) she's done it herself due to finding a good deal. I think the airlines are getting a little better at selling all their allocations and dropping their prices accordingly.