hi there
はじめまして
I'm Japanese, so I can't use JR Japan Pass so don't know much about it,
but I used Eurail Pass when I went bacpacking in Europe and I tried hard to figure out what the best way to use it, so I guess I understand how you feel
Can you tell me how much the prices for 1 week, 2 weeks, 3 weeks are?
There are also lots of good package deals including accommodation and transport here.
There are coach(long distance bus) services with reasonable prices too.
When I travel, I use coachs and the local trains often cos I enjoy all the sceneries and meeting local people on the way.
Anyway, I hope you have a safe and wonderful trip !