I can't seem to find a map that includes every railway in Japan (it's very very difficult, actually). Is there a map (as photo) that includes every single railway, except google map?
Here you go: 全国鉄軌道路線図
￥1,296 from Amazon.co.jp. Here's a blog review with some pictures of the map folded out.
And yes, that's entirely in Japanese, I very much doubt such a thing exists in English. To get some idea of the effort that would entail, here's a closeup of another incomplete & partial map covering just the Tokyo metro area.
Railway tracé by number of tracks: http://www.itoworld.com/map/14?lon=140.62370&lat=38.79141&zoom=5
Railway tracé by clearance, gauge, number of rails: http://www.itoworld.com/map/15?lon=140.62370&lat=38.79141&zoom=5