hey just thought i'd take the opertunity to say that my return flight that i booked on statravel.com cost aobut £580 inc tax; that's a filght leaving early july, returning early august, with a stopover in seoul(i think it's about 17 hours total for the flight). I'm sure i could get cheaper but i wanted to get it booked so i couldn't put it off again. you're going for a simillar amount of time to me, so what i'm doing is 1.5 weeks tokyo, 2 weeks going south to see some more cities on the train. I reccon that it's a pretty good balance, have a bit of time to adjust in tokyo, then go see the sights around the south for 2 weeks, and than hang out in tokyo again, see the sights, maybe go on some trips out of the city
i've booked my first few nights in tokyo just because i like knowing where i'm going, and i reccon it will save me a few quid(it's under £9 a night if you've not had a look at what's on offer). other than that for money saving, erm try to stay in hostels with a kitchen area, that should save you a fair amount of money pretty quickly, also if your going for the 2 weeks on the train that i mentioned then the rail pass is a must