If you're looking for just some quick trips around Japan to the major tourist sites, check out the following packages:

http://www.jtbgmt.com/sunrisetour/

The best deals are under the 'Free Plan' section - these are self-guided packages that include hotel and transportation via Shinkansen.

I've done both the Kyoto 2 day package for 19,000 Yen and the Kyoto/Hiroshima 3 day package for 36,900 Yen. Both are good deals when you consider how expensive train tickets are here in Japan.

With a student visa, you should have no problem being getting these packages.