Me and the wife did a 10 day trip over there out of ATL a few months ago. It was Cherry blossom season so the loads were tight... but yea everything said above is solid.
We also did the Arakura Sengen Shrine out of Tokyo as an easy day trip at the last minute. Very simple to get around if you get the rail pass and you can buy it at the Narita airport. The cost is a little more if you buy it the day of but with non reving you never quite know if or when youll arrive.
Have fun!