Japan travel help?

Hi

my girlfriend and I are travelling to japan on 21st march to 13 april 08. we fly in to tokyo and plan to see as much of japan as possible in 3 weeks going from tokyo-kyoto-osaka-hiroshima and then up to hokkaido. What would be our best and cheapest travel options? JR pass? Flights? Buses?
Any recommendations would be greatly appreciated.

Many thanks

you need to use the JR pass for at least 7 days with a base some where

I did a cross country trip, in two weeks, with the JR Green pass because I had a large backpack (and thought I would need the extra leg room) but a eregularf pass would work.
http://japanrail.com/index.html (I suggest you read whole website, if you havenft already)
http://japanrail.com/JR_tourismlinks.html http://japanrail.com/JR_timetableandfare.html (couple key sections of website that I suggest)
Kagoshima, Nagasaki, Hiroshima, Kyoto, Chiba and Sapporo are couple of the cities I visited, I missed Shikoku island, and stayed in a new hotel each night/city. The only problem with my trip, staying at new hotel every night, is I was running around too much between etourist sitef and finding hotel to fully enjoy my trip.

I suggest 3 or 4 base sites (Hiroshima, Osaka, Chiba, Sapporo). As for hotels I stayed in Tokyo-Inn, Comfort inn, etc, at 6800 yen ($60-ish Canadian) per night (single person), another cheap option is hostels.

The only other way to make your trip as inexpensive as possible, is to plan your butt off. Find the etourist sitef that are interest of you, in said city, and find location (address is best) in relation to the train station (bus terminal, witch ever you choose) and decide if the distance is walk-able for you and your girlfriend. Otherwise see if there is another train stop, local train (still on JR line), that is closer.

Have a safe trip

Thanks for your responses, they're very helpful. Having a few bases sounds like a really good idea. May have to do some extra planning so we don't spend too long looking for places to stay and missing out on the sights.

I would consider rail passes for Honshu and flying to Hokkaido, using an air pass:
http://www.japan-guide.com/e/e2364.html