For those just visiting Japan as a Temporary Visitor there are special air passes for those taking JAL or other One World carriers called a Yokoso/Visit Japan Fare.
For taking any international carrier, there is ANA’s Visit Japan Fare and JAL has its version, called a Welcome to Japan ticket.
Take the 1000 yen bus, or if going to or near one of the expensive tourist hotels, there is the orange limousine bus (though it’s the most expensive way). From Narita the Keisei and Narita Express are 2 popular trains used into Tokyo.
For using the latter, there is also a special discount round trip N’EX ticket (valid up to 14 days).
Some ear-plugs, an eye-mask, and skin lotion can also help.
Before your flight, sign up with a frequent flier program — many airlines have them, and eventually you can get free flights through them.
Autumn is by far the best time to visit Japan, as far as the weather goes.