14D in Japan

Day 1: Arrive in Narita
Day 2: JR Train to Oita and stay there, stopover at Mojiko.
Day 3: Day trip to Nagasaki
Day 4: Day trip to Beppu and Yufuin
Day 5: Oita to Hiroshima and stay there.
Day 6: Miyajima
Day 7: Hiroshima to Koyasan and overnight
Day 8: Koyasan to Shin Osaka and stay there.
Day 9: Kyoto and Saga Arashiyama
Day 10: Shin Osaka to Kawaguchiko and overnight
Day 11: Kawaguchiko to Tokyo
Day 12: Day trip to Kamakura & Yokohama
Day 13: Shopping in Tokyo.
Day 14: Leaving Narita by a night flight.
Thank you.

Day 1: Arrive in Narita
Day 2: JR Train to Oita

You really don't want to do that. Jetstar will fly you there for 7000 yen (and ANA for 10000).

Also, day-trip to Nagasaki from Oita? That's at least 4 hours one way.

I did consider a domestic flight to Kyushu.
The flight is about 2hr. Taking the time required to get to the airport, check in, clear immigration and get out of the airport, the time saved is probably half as compared to taking the train with my JR pass.
As for the day trip to Nagasaki, I will start early to reach Nagasaki around 11am and returning to Oita around 6pm, leaving me about 7hr to see the main places of interest in Nagasaki.
Thank you.

Not sure exactly what you trying to ask, but it is sure a typical itinerary of "I've been there!".

Hi Jack. I've travelled Japan quite extensively and my biggest suggestion is to try and stay to one general region for two weeks. A general region may be a place like Tohoku or Kansai. Staying two nights in one location and only travelling an hour or two a day (because locations are closer) lets you get a lot more bang for your buck.

The locations you have chosen are definately doable - but I'm not sure if you'll enjoy it as much travelling so fast.

But just remember - I'm only one voice so take it with a grain of salt...

Hi Jack
Appreciate your reply.

However, I do want to spend at least 7-9 days in Tokyo.

Do you have otherwise plan for a short stay in Osaka, Kyoto or Fukuoka?

Look forward to hearing from you again.

Thank you.

Kind regards
J

The duration at each location is dependent on your preference.