Japan-savvy friends, please help!

[raspberrypi]

My dear F-list! I have three hours to submit a proposal to my mother convincing her my friend Alice and I are well planned adults (we're twenty already...) and can handle traveling by ourselves to Japan without getting lost/stranded/killed.

If you know of
- A nice and cheap hostel or hotel in Tokyo and/or Osaka
- A good comprehensive online guide to the transit system in Japan
- Any good online guides for traveling in Japan, period

please let me know asap! ♥