Traveling in Japan DIY is very easy. Links for JNTO and japan-guide were posted before. There's a link which you will find useful when taking trains in japan. A route planner in fact.
http://www.jorudan.co.jp/english/
You need not be too tight in the bugdet. Give you an example of 2 couples for a 10day F&E spring trip to Kyushu:
JR pass 7D @ Y23,800. Total expenses covered by my pass using JR lines if paid by cash would come to Y76,000 (the amount covers only the limited express and shinkansen rides with reserved seats; local line rides not included)
Accomodation for 2pax:
6N Hakata @ Y12,500 with Bft; 8min walk from rail stn
1N Kumamoto @ Y21400 with Bft; 3min walk form stn (weekend rate, higher)
2N Beppu in a ryokan hotel @ Y32,400 with Bft and Jap style dinner; 10 walk from stn
Expenditure, including 7D JR pass, 9N accomodation, local transport, admission fees, meals came to about S$2100 (under Y34,000 pax). Airfare by SQ not included cos that depends on what's offered. SQ fly direct to Fukuoka in Kyushu.
Places visited: Hakata, Daizaifu, Nagasaki, Oita, Beppu, Kitsuki, Yufuin, Mojiko, Kumamoto, Hiroshima, Miyajima, HImeji.
Tips:
1. Must do your research and plan your travel carefully
2. >95% of names of places in japan are in Kanji. So it's best to have japanese language maps. Many of the local signboards are written as such. If you can read Kanji, moving around will be much easier. However romanised japanese are found on many signboards.
3. Information counters are found in almost all the rail stations and you can buy local pass there too or they will advise you
4. Buy a local city transport pass for a day unlimited travel
5. Food prices are posted outside the restraurants... so no embarrasment to check out.
6. Meals around train stations and local eateries are reasonable
7. For budget planning purpose:
a. Meals (L/D) Y1000 per meal
b. Local transport Y500 per day
c. Sight-seeing Y500-1000 per day
d. Odds and end Y500-1000 per day
Japan is not a cheap place, but you can manage the cost of a pleasant holiday. Hope the info helps.