I'm hesitant to convince someone to do something that they aren't very interested in doing. So if you are skeptical at all just postpone the weekend getaway for a time when you know that you have the time off, the money, and most importantly the desire.

However to answer your questions about safety-you couldn't pick a safer place. About the scariest thing that could happen would be an earthquake and the odds of that are pretty small

As for hotels and money, if $$$ is tight you may not want to go to Tokyo. This is a city that sits near the top of the list of "the most expensive places on earth to be" so you may want to explore lodging costs before making a flight reservation.

As for the coach thing, if you normally enjoy flying up front I would not be looking forward to Y on a JFK-NRT flight, you know yourself better than I but it sounds like you may want to get your hands on some VIP's before you go (if you do).