Once you get here you'll find it's like most places - if you know what you're doing it will be easy and cheap; if not, it won't. So, for the budget, I recommend planning:
$30 - $40 per night cheap hotel
$45 - $90 per night business hotel
$90 or more for Brand hotel (Hilton, etc.)
$50 per 1000Ks by bus
$150 per 1000Ks by Shinkansen train
$150 per 1000Ks by rental car.
$100 - $300 per 1000Ks by plane (depends on when/how far in advance it's booked)
$3 per meal for instant crap/McDonalds
$10 per meal for standard Japanese/Chinese meals
$15 - $25 for nice Japanese/Western meals
$50 - $100 for French/high end restaurants
As for what to do. Japan isn't like Egypt. You can't go to Egypt without seeing the pyramids/nile, etc. You can come to Japan and do this or that - or nothing or everything - it's all much the same. Your goal should be to just get a feel for the place, note how things are done differently, see what the lifestyle is like, and try to enjoy the atmosphere of the different places/cities you go to. But generally speaking Japan is like a Thai 'lady-boy'. If you try to see a woman you see a boy, if you try to see a man you see a woman. You'll understand what I mean after you get here.
Suggested things to do (with $6000) budget (remember prices are much the same as Sydney):
Fly to Narita (Tokyo Int airport)
Spend first night/s in Tokyo (if you need a cheap place let me know and I'll recommend one)
During the day go to:
Akihabara
Tokyo Tower
Shibuya
Shinjuku
Ginza
(All these places are on the same train line and easy to get to. There's nothing special to do - just walk around. Costs about $2.50 per train ride)
Day trip:
Go to Kamakura
About a one hour local train trip from Tokyo
Easy to get to, famous, and free. All you have to do is walk around as much as you like and look at things. (You could wear your Indy clothes too - Western clothes in Japan are all costumes).
Day trip:
Yokohama
About half an hour from Tokyo. Just walk around, go to Chinatown if you like (it's crap) have lunch, go to Sakuragichou (one stop - 4 minutes) it's nice - walk around.
Day trip:
Kawagoe
This place is famous for old style traditional houses. It's a one hour trip from Tokyo (costs about $5.00). Walk around a look.
Next go to Nikko.
About a three hour bus trip. See the temple and walk around. Take your whip because there are monkeys. It's about a $5 entry fee, the bus is about $25.
Next go to Kyoto.
Look around and stay a night or two.
Next go to Hiroshima.
As above. You'll love it - they're friendly and it's easy to understand.
Next go to Kyushu.
Fukuoka and Nagoya.
Choice:
Back to Tokyo or fly to Okinawa or some other island
From Tokyo get the night train to Hokkaido.
Costs about $150. Look around, play with the cows, and take your whip - there are Russians.
Fly back to Tokyo - stay until you have no money and then go home.
I could do all that for just over $1500 Australian but you will probably make some mistakes and also want to buy crap stuff so it should cost you about $3000 - $4000.
Cheers,
Rob