Japan - Depends, have a idea of what theme or what you would enjoy.
Plan where and how long you wish to spend in each area, Island or Prefecture, budget, etc
JNTO website and physical locations are great resources, JETRO and other Ancillary organizations, as well as NHK should provide helpful, but biased views. Just be aware, it's free for a reason.
Yes, In Tokyo, JR Yamamote Line is important. The Tokyo Metro 2 or 3 day unlimited pass for tourists when offered are a sensational bargain, remember MOST cities or smaller regions also offer these for Metros, buses, other transport or "local tour buses." As MARKED discounts, but may be limited in scope to tourist areas, which you are interested
JNTO, if you can get to a physical location, has wonderful handouts in most languages of countries they are targeting. The also are a venue for flyers, pamphlets of deals, etc, there will be lots to wade through, plus FREE MAPS, good to get Hands on physical maps to study BEFORE you leave!
It will be easier to study the maps a bit BEFORE you arrive. It won't solve all your problems, but it will help
The web is wonderful, since most, even small towns or regions have a presence... BUT some may be inaccurate or not updated frequently enough! Carpe Diem!
Subways are reasonable, Taxis are darn expensive.
YES< JR Rail Pass is a steal, be aware there are 2 basic types:
The Nationwide one, that you can only buy in YOUR country or the "local/regional" ones that can be had in Major JR stations of that particular "regional JR" Japan Rail, is like a United States of Railways. You may have only heard of the one you can buy in your home country, it's been perhaps recently the downturn in the Japanese economy and Yen had necessitated this strategy, More online, at the "separate JR's" besides the BIG JR East, also physical literature, read pamphlets at JTNO when available
Renting a bike has been a wonderful option, my last 3 times in Japan. Twice biking in the Tokyo area, and once in the Seto Island Sea Bridge Area. Japan is bike friendly. Please be aware, Bike insurance is not available, if you HIT someone, while riding on your bike! YOU will assume FULL Financial burden IF YOU HIT A pedestrian when on a bike!!! And maybe Criminal! SO be careful! use the "bells" and its fun!
Walking is a good way too, but if you are short on time, the other two methods are best, unless someone is shuttling you around in their private vehicles!
Business Hotel Chains, offer a safer alternative to the Youth Hostel scene, if you can afford little above the Hostel price nightly, you will have privacy, your our bathroom, etc although small... Remember you are in Japan, most things are small. With a frequent customer card, most give the free night with 10 nights paid. They are clean. courteous, well informed, and consistent throughout the country.
Good Luck, I could go on... but, my pillow calls...