12-day - any alternatives or adjustments?

We (my daddy and I) will be flying in and out of Narita (Tokyo) on 24/6 and 5/7. I would appreciate any feedback or advice for any necessary changes. My planned itinerary is as follows:

24/6 arrive at Narita International ~17:25 (overnight in Tokyo)

25/6 explore Tokyo (Tokyo)

26/6 day-trip to Yokohama (Tokyo)

27/6 day-trip to Kawaguchi-ko (Tokyo)

28/6 (start using JR 7-day Pass) travel to Nagasaki, catch the night view at Inasa-san (Nagasaki)

29/6 sightseeing in Nagasaka in the AM, travel to Hakata in the PM, explore the city – since likely to omit Kumamoto castle (Hakata)

30/6 day-trip to Beppu & Yufuin (Hakata)

1/7 travel to Miyazaki, drop off luggage at hotel, visit to Aoshima (Miyazaki)

2/7 day-trip to Takachiho Gorge (Miyazaki)

3/7 day-trip along Nichinan coast to see Udo Jingu & Sun Messe, travel to Kagoshima (Kagoshima)

4/7 explore the city in the AM, (last day of JR 7-day Pass) travel to Tokyo in the PM (Tokyo)

5/7 explore Tokyo before heading to airport for ~17:30 flight home

I realise that there is a lot of time spent on commute in this itinerary, but we will be taking the train since driving isn�ft an option for us. I would really appreciate any advice or suggestions for alternative routes that might work better.

I am also wondering if we should substitute our Kyushu portion of the trip with another part of Japan that might be better than spending 8 hours each way on train travel between Tokyo and Kyushu (not to mention the train travel within Kyushu), however, I don�ft really know where as I am not familiar with the central part of Japan.

We have already been to Osaka, Kyoto, Kobe, Okayama, Nara, Shirakawa-go, Takayama and Sapporo, Otaru, Asahikawa, Furano, Biei, Hakodate, Toya-ko in Hokkaido.

We enjoy sightseeing (historic and natural), cultural experiences, comfortable atmosphere, just a bit of shopping and good food.

Sorry about the long post. Thank you in advance for your help & advice!

Why not fly to Kyushu instead? You might find it's cheaper than the cost of the rail pass, then check out if the Kyushu Rail Pass will work for you: http://www.japan-guide.com/e/e2361_05.html

Also, I recommend staying the night in Takachiho if you're using public transportation. The nightly Yokagura dance at Takachiho Shrine are one of the highlights of the area, but you probably wont be able to make it back to Miyazaki if you stay for it.

You cannot do Beppu and Yufuin together in the one day with omitting a lot of good sights.

And the time in Kagoshima is not enough time to see anything either.

I would consider only doing the northern Kyushu destinations in an effort to have more sightseeing time. And flying tokyo to hakata and back.

You just don't have enough time or days to see both Kyushu and Tokyo.

That was my question as well. To take the bullet train from Tokyo down to Hakata and then another train down to Nagasaki would murder almost the whole day, taking a minimum of 8 hours 20 minutes. You could fly down using ANA's Experience Japan Fare for just 10,800 yen one way, and take less than 2. You would need to take a bus from the airport to Nagasaki downtown though, about 45 min and 900 yen. You could also use it from Kagoshima back to Tokyo.
Or if you want to save money, there is a low cost carrier like Spring Japan that flies from Haneda, Tokyo to Saga for as low as 5700 yen one way, and then after a short trip to Saga Stn you'd take a 75 minute train ride into Nagasaki. (About 3,360 yen one way for non-reserved seat).
Going to Hakata is about 2 hours. There are some good places to see. At the very least, the Nanzoin Temple is superb.
http://www.thejapanfaq.com/fukpic.html
https://www.youtube.com/playlist?list=PL7LcPcmoSg-j4RLa6iC7ayvBAbOn8-0...
Both Beppu and Yufuin are famous for the hot springs, though Beppu has more variety.
https://www.youtube.com/playlist?list=PL7LcPcmoSg-hOggZamc2lUNTr46ApKX...
I'd also recommend an overnight at Takachiho - it is quite isolated and buses there are infrequent. Kagoshima has some sights, but the real treat is Sakurajima.
https://www.youtube.com/playlist?list=PL7LcPcmoSg-irtXXB8IJMdkB9mF0qjn...
Again, with such a distance, flying makes so much more sense.

I wouldn't do Aoshima, followed by takachiho and then back to Miyazaki. Spend a day for takachiho and then two days in Miyazaki. This is as the travel time is a lot!! This would make seeing Miyazaki and then traveling to Kagoshima in one day impossible.

I also like the "fly to Kyushu" Idea, but that might not be what you want to do.

If you really plan to do the Tokyo to Nagasaki trip in one day, I would flip your day trips in Tokyo a bit, and spend the final day in Yokohama so that I could overnight near Shin-Yokohama Station.

The reason for this is that is a 6:00AM Hikari Shinkansen out of Shin-Yokohama that is bound for Hiroshima. Get off at Shin-Kobe and catch the Sakura Shinkansen for Shin-Tosu. The Sakura arrives four minutes after the Hikari arrives at Shin-Kobe Station, but you should be at the same train platform. You will have more time to make the transition from the Shinkansen to a Limited Express for Nagasaki. You will end up in Nagasaki around 2:30 PM, which will give you a little time for sightseeing.

I would actually advise against this, and I would fly a discount airline from Tokyo to somewhere in Kyushu. I would also try to head to southern Kyushu and then make my way back towards Tokyo. Jetstar for instance, flies into Fukuoka, Kumamoto and Kagoshima. Currently, a Jetstar flight from Tokyo (Narita) to Kagoshima is 4590 yen on June 28th. If this flight gives you an extra day on your JR Pass, that extra day of the pass could be used to ride the NEX (Narita Limited Express) from Tokyo to the airport, which costs 3220 yen.

If you fly into Kumamoto:

Since you are planning to to Takachiho, you could catch a bus from Kumamoto to Takachiho, and delay activating your seven day pass a day. As Jh suggested, I would spend the night at Takachiho, and go watch the Kagora dancing at the shrine.
When you return to Kumamoto, travel south to Kagoshima, and then head for Miyasaki.

If you fly into Kagoshima:

Spend what time you want in Kagoshima, and then head for Miyazaki. After visiting Miyasaki, head north towards Beppu, and stop in Nobeoka. Catch the bus to Takachiho and spend the night.

Whichever way you go, head up to Beppu, and then go to Fukuoka and Nagasaki.

Saving the extra day on your 7 day pass would allow you to take the NEX limited express train to the airport. It would also mean that your could stop somewhere on the way back, say Himeji or Kyoto, for the evening.

If you decide to fly into Kagoshima, consider going to Yakushima Island for a day. Once again, you could do this before activating the 7 day JR Pass.

I am hoping to help you open your options. Good luck with your planning.

Thank you for all the advice, very much appreciated! I am processing all of it and seeing it I can make things work better.