Welcome to FT. May I ask your reason for going to Japan?
I can't give you Japan specific info (I'm sure others will).
In general travel trip...I prefer an aisle seat so I can easily get up and walk around/visit the restrooms. Dress comfortably. Buy an inflatable travel pillow, eyeshades, and earplugs. Carry on only what you need/things of value. Buy a huge bottle of water to bring along, as flying and in particular long haul flights are quite dehydrating. Don't plan much the first day as you'll have serious jetlag. You may want to take a sleeping pill once on board to get the most sleep you can.
Best advice is if you have questions, ask someone. You'll more or less be herded through baggage claim and customs along with everyone else, and if you don't know what to do just ask someone, either a fellow traveler, a flight attendant, gate agent, whoever.
Even after many flights, I still find it an adventure at times. Just roll with it, you'll have an awesome experience!
Oh...and wear shoes that are comfy and easy to get off and on...trust me