Will a Japan Rail Pass allow me to travel anywhere in Japan?

Hello Yemen, The Japan Rail Pass allows you unlimited travel on almost all JR trains, including the shinkansen (excluding the Nozomi superexpress) in all regions of Japan. If you plan on travelling all over Japan then this pass is worth getting. If you plan on only travelling in a certain region in Japan then it might be worth getting a region specific pass. The Japan Rail Kanto Area Pass is a new pass that allows you to travel in Tokyo and the surrounding Kanto region including popular tourist destinations such as Mount Fuji, Hakone, Izu, and Karuizawa. The Japan Rail Kanto Area Pass http://japan-australia.blogspot.com.au/2012/01/japan-rail-kanto-area-pass.html To figure out if a JR Pass would be worth it or not for you, use Hyperdia’s website http://www.hyperdia.com/ to figure out how much your planned trips might cost, and compare it to the cost of a JR Pass.

Yeah, if you want to travel all over, you need both passes. Check to see where you want to go first, and try to make all your destinations do-able on one pass, and buy the one destination a la carte, if it's the only place in the other region that you want to visit, but not worth it to buy the entire pass. There are many other lines that's not JR, but local rides aren't that expensive (hopefully for you).

No.

You can use it in all regions in Japan. But you can use it only for JR trains. There are many non-JR train lines in Japan. It's good only if you take long distance trains many times.