Navigating Japan Transit
English Trail Guides
Traildino is a trail hiking database that offers some basic information about trail. It has a few of the GPS maps listed but it is very scant in this area.
Navigating Japan transit can be tricker if you are trying to get back into town for supplies. The buses run very infrequently out in the country. I have not found a website that has bus schedules in English. My recommendation is if you need to get into a town from out in the middle of the hike is look for a bus that is going to a station or the symbol. (駅)
I have provided some links to websites that can help you navigate the best way to get around in Japan using trains, highway buses and the subway.
My Trip Along the Tokai Nature Trail" is a blog from a man who hiked the trail in 1976. It is a great read and gives you a wonderful perspective about what hiking the trail was like.
My Trip Along the Tokai Nature Trail
"A Rough Guide to Walking the Tokai Shizen Hodo" is the guide that I used before setting out. It does have the GPS coordinates for most of the trail. I did not use them, but I thought I was going to before my trip. It is a guide you should absolutely read before setting out.
A Rough Guide to Walking the Tokai Shizen Hodo
Train Routes
Hyperdia offers timetables and route search for railways in Japan, in Japanese, English and Chinese. There is also Japan transit planner Jorudan. Between these two I think it is just a matter of preference as to which you prefer using.
Highway Buses
Highway buses are a great way to travel long distance in Japan, for example getting back to Tokyo form Osaka. The highway buses Japan site helps you make reservations in English. There is also the night bus site Willer that offers cheap long distance fairs.