NRT is a great place to go to... Traveling alone is nice especially if you need time to be by yourself and think. It's very safe in Tokyo, but the prices can get kinda steep.

There's plenty to do depending on your interests... shopping, sightseeing, hot springs to name a few...

It's a modern city with lots of culture...

12-13 hours in Y isn't too bad (bulkhead would be nice) unless you are used to Business then that's a different story.