I traveled to NRT last year. Out of ATL nonstop on DL and back on AA to DFW. No problems with either flights....but it was in October! Anyway, I can't be of much help on flights for you, but I do second the idea of a Japan Rail Pass. THe shinkansen are amazing and, while the pass was about as much as our nonrev tkts were, it is worth it, and the travel experience is calming, efficient and fast! You do have to purchase the pass in advance here in the US, though, so plan ahead!

Hiroshima was a highlight of the trip, but I would try to get out and see as much as possible, a day of bike riding through Kyoto was an unexpected delight for me.

Happy to help as I can!

-Marty