Japan's bullet trains are as awesome as they sound. You can zip from Tokyo to Hiroshima in a few hours, and every train is sparkling clean and leaves exactly on time. The efficiency is all the more impressive because so much of the system is human-powered, rather than automated.
Not all of Japan's trains and transport links are high-speed, however. To get to Koyasan from Osaka I needed to take an 80-minute train ride that met up with a funicular that met a bus. Getting to Kyoto from there required about six different connections. Fortunately everything is clearly marked and there's always someone to help, so figuring out what train I needed to get on and where I should be sitting were much easier than they would have been anywhere else in the world.
Here are some tips for booking and taking your high speed rail trip in Japan:
Before Your Trip
Get a Japan Rail Pass Before You Leave for Japan
You can order these online, but if you're moving around before your trip like I was, you may need to find a nearby travel agent that sells them. I went to the JTB agency in the Fairmont Hotel in Vancouver a few days before I flew out and got a 7-day Japan Rail Pass (for all of Japan, vs. just JR East). I also bought my ticket to the Studio Ghibli Museum while I was there.
Activate Your Pass When You Book Your First Trip
You don't need to activate your pass immediately, although you can do it at the airport if you're starting right away. When I had a plan for how to use my 7 days to travel outside of Tokyo I took my voucher, my passport (you need your visitor stamp), and the time and number of my first train to the JR ticket office in Tokyo Station. They give you the actual pass to fill out with your info and the date it's starting. Then you can start booking train tickets.
Look Up Your Trains Online
You can't book trains online but you can check the timetables and plan your trip ahead of time. JapanRailPass.com has a great guide to using Hyperdia, the online timetable.
Don't Forget Your Return Trip
I miscalculated and left my trip back to Tokyo out of my 7-day trip, as well as my trip from Tokyo city center to the airport, which can also be covered by a JR pass. I took a sleeper bus back instead.
During Your Trip
Get Into Place on the Platform, but Don't Board Too Soon
There are signs and platform markings to indicate where you should stand for your car number, and someone on the platform with flags to indicate when the trains are arriving and leaving. Just make sure the screens say your train is next, because these are fast trains and there might be one arriving a few minutes before yours.
You Can Hop On and Off and Book Reserved Seats the Day Of
For example, I took the train from Hiroshima to Himeji, reserved a seat on a train to Osaka for later that day, stuck my bag in a locker, and went to see Himeji Castle and Kokoen for a few hours. There weren't any reserved seats left for my entire trip to Osaka so I sat in an unreserved seat until my assigned one freed up at a later station.
Pick up an Ebiken at Least Once, but It's Not Required
I had one and like everything I ate in Japan, it was delicious, but unless you're collecting them as gifts you can also get a decent lunch for less at a convenience store.
Trip taken November 2015.