If you’re going to Japan any time soon, this is a ‘must’ read.
We managed to figure it out pretty well, but this post definitely would have been a god-send about 3.5 weeks ago ;D
Enjoy!
The variety of trains and train companies in Japan can seem complex to visitors, and I’m not going to lie to you: it is. What it isn’t is impossible, and fortunately I am a huge train nerd, so buckle in and I’ll walk you through it.
Train Companies
The main operator is Japan Rail, or JR, but JR is actually a group of smaller companies: JR East, JR West, JR Central, JR Kyushu, JR Shikoku and JR Hokkaido. Unless you are using a regional-only JR Pass, you really don’t need to worry about this, and may consider them all to be JR.
There are many smaller operators, running everything from an entire regional network to one tiny line that services a handful of stations. These are often owned by a department store, oddly enough, and came about as a way of helping potential customers reach a specific shop. Trains…
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JaPlanning 
Thank you for your kind words. Really, if this article helps just one person with the trains it’s worth it 😀
No worries at all! It’s very comprehensive and you are very right about how scary it all looks vs. ease of use.
Sometimes it actually boggles my mind that the train system is SO HUGE but has been made so accessible and intuitive to use. Also glad! ;D