Flights may be $1080 thru Jetstar but as soon as you add the Shinkansen to Tokyo you add $300 on top. If you just want to go to Osaka Jetstar can't be beat. Of course you can get a JR Pass and use that for the shinkansen so you gotta factor all that in your research.
My TAS2008 flight is $2021 JAL direct Sydney -> Narita. I paid a lot to be fully flexible, direct, on one of the most popular days and be the best flight time (JL772).
As a comparison, Jetstar for the same day was $1800 all up including meals, entertainment (I know if I didnt pre-buy all that I would have bought it on the plane cause i like that stuff) and shinkansen to Tokyo. Add on top of that all the farting around with baggage and trains and I decided no thanks and paid the extra $200.
As for research on Japan try these links:
English Japan rail trip planner site: http://www.hyperdia.com/cgi-english/hyperWeb.cgi
This site has every rail timetable, govt bus timetable, domestic airline timetable, fare cost schedule programmed in and will tell you to the minute how to get from one place to another.
Japan Rail Pass Site: http://www.japanrailpass.net/eng/en001.html
English site on the JR pass, costs, conditions, etc.
Kakaku.com http://www.kakaku.com/
Best site for finding street prices for electronics in Japan. It's in Japanese though. Learn katakana and it's not too hard to navigate.
Jalan.net http://www.jalan.net/
Best site for booking hotels in Japan for the Japanese domestic tourism market. I get consistently better prices here than anywhere else on the net. Usually you do not have to pay in advance for Jalan bookings either. Again it's all in Japanese but if you mess with the site enough you can find out what to click by trial and error.