Japan Rail Pass Guide

First lets start with the fact that there are many JR passes. There is the JR national pass that covers the entire country (probably your best option), and then there are regional passes. I would recommend the national pass, as it will probably pay for itself. However, if you’re not doing any long train rides you may find the regional pass better suits you. After looking at their pricing I’m not sure regional passes are ever a better option, however it’s always worth a look. 
The national pass has three options: 7, 14, or 21 days (consecutive) priced $254, $405, $518, respectively. The 21 day pass is a STEAL if you plan on traveling all over Japan. For the cheapest prices order your pass ahead of time, it is slightly more if you purchase your pass inside the country. To my knowledge the Japan Rail pass covers most JR forms of transportation. This includes the metro, some local JR buses, JR Miyajima ferry, etc. However it does not cover anything that is not JR operated. The pass also limits you to three train lines: Hikari, Kodama, and Sakura. You are not permitted to ride the Nozomi or Mizuho lines with the Japan Rail pass. You can reserve a seat if you would like with your pass, or just board the unreserved section of the train. The Green section is not included unless you have paid extra for it.
You can figure out which trains you can ride through the timetable. As this can be tricky to read let’s break down how to understand it. This is just one of the timetables, but it should give you the ability to read all of them. First lets start with the basics. We’ve already discussed on the Japan Rail pass you can only board certain trains, here’s how to find them.
Japan Rail Pass
N is Nozomi, H is Hikari, K is Kodama, M is Mizuho, and S is Sakura. You are able to ride the H, K, and S lines, see marked at the top of each column in the red box. You will see each column is marked by one of these letters and a number, that is the train number so when you get to the platform you will see train 561, for example, and know that is your train. They do not change (unless this schedule has changed). Numbers help to ease the language barrier. Now, this is a westbound timetable, hence why Tokyo is at the top of the list, but note not all trains start at Tokyo. 
Let’s go through an example. Let’s say that you want to go from Tokyo to Kyoto and you want to leave Tokyo at 10am. First let’s find Tokyo, see the red boxes on the image below.
Japan Rail Pass
Now that we’ve found Tokyo, read to the right until you find approximately 10am (see box on image below). The table below the first is a continuation.
Japan Rail Pass
Now, we see four trains in the box labeled K, N, H, N. The two N’s are off limits (Nozomi), so now we have two options to get to Kyoto. 
Japan Rail Pass
Look down each column until you get to the Kyoto line (boxed in blue). K 645 leaves at 9:56 and arrives 13:36 versus H 467 which leaves at 10:03 and arrives at 12:46, hence in terms of speed the H 467 train would be your better option. 
Hope this guide helps!