10-12 day Kyushu trip. Suggestions?

I'm planning on traveling down to Kyushu in March, and have come up with a tentative itinerary, and had a few questions about it:

First the itinerary:
1)
train overnight (moonlight nagara)
2)
Hiroshima, train over to Fukuoka? (moonlight kyushu?)
3)
Fukuoka
train over to Aso
4)
Hike Aso
train down to Kirishima
5)
Hike Kirishima
Kagoshima
down to Yakushima
6-8)
Yakushima
9-10)
Miyazaki
Takachiho
Udo Shrine
train over to Beppu
11)
Beppu
train back up to Fukuoka
11-12)
Night train back to Tokyo

First of all, I would like to keep it as close to 10 days as possible, so I'm thinking of taking out either Kirishima or Mt Aso. Preferably Aso, but any suggestions on which would be better?

Would it be possible to see Miyazaki and the area all in one day, rather than 2?

Also I was told that the Moonlight Nagara will be running beginning the 13th of March, is that the same for the Moonlight Kyushu?

Lastly, would it be crucial to book rooms in every city, or will I be alright just showing up on the day in some smaller towns? I would like some flexibility while I'm on the road.
Also, can you stay the night at train stop waiting rooms or something, or will they kick you out?
Other general suggestions/inputs would be very much appreciated as well regarding the itinerary.

Thanks in advance.

I havent been to Kirishima but I have been to Mt Aso. From the photos of Kirishima it looks pretty similar to Aso in terms of scenery but I loved going to the volcano in Aso so I would leave that in if I was you. Make sure you check out the bus times to get there from Aso station as they arent very frequent.

I am afraid your itinerary is utterly impossible. It contains multiple non-existing train rides and is generally way too packed.

1)
train overnight (moonlight nagara)

Seat reservations are mandatory on the Moonlight Nagara. There is a high probability that the train will be completely booked out several days before travel date. Make sure to secure a seat reservation in advance, otherwise, there is a high probability that you won't be able to ride the train.

Hiroshima, train over to Fukuoka? (moonlight kyushu?)

The Moonlight Kyushu does not exist anymore.

Hike Kirishima
Kagoshima
down to Yakushima

Too packed for a single day. The last ship to Yakushima is at 15:50. The last flight from Kagoshima Airport (close to Kirishima) is at 17:00.

A rental car is recommended for Kirishima National Park, as public transportation is virtually non-existent for access to the hiking trails:
http://www.japan-guide.com/e/e4626.html

Night train back to Tokyo

There is no night train between Fukuoka and Tokyo! But there are overnight buses.

First of all, I would like to keep it as close to 10 days as possible, so I'm thinking of taking out either Kirishima or Mt Aso. Preferably Aso, but any suggestions on which would be better?

As you can see, your itinerary contains some major transportation related problems. You have to solve them first of all. For time efficient travel, I recommend to fly (with an air pass). And to use a rental car in the regions where public transportation is bad or non-existent.

For example:

Tokyo - (air) - Beppu - (rental car) - Aso - (rental car) - Takachiho - (rental car) - Miyazaki - (rental car) - Udo Shrine - (rental car) - Kirishima - (rental car) - Kagoshima Airport - (air) - Yakushima - (air via Kagoshima Airport) - Tokyo

Would it be possible to see Miyazaki and the area all in one day, rather than 2?

No, it is impossible. Miyazaki is one of Japan's largest prefectures and transportation is slow.

Also I was told that the Moonlight Nagara will be running beginning the 13th of March, is that the same for the Moonlight Kyushu?

No, the Moonlight Kyushu has not been operating in years. Just wondering: where do you get the information about the Moonlight Kyushu?

Lastly, would it be crucial to book rooms in every city, or will I be alright just showing up on the day in some smaller towns?

Just showing up without reservations translates into time loss during your trip and an uneasiness about not being sure whether you will find a room in your budget range. In the worst case, you will find yourself without a room at all. I recommend to make all reservations before you leave for Japan or at least one day in advance.

Also, can you stay the night at train stop waiting rooms or something, or will they kick you out?

At some stations it might be possible, but the locals will not appreciate it. It is not an acceptable thing to do in Japan. So, I strongly discourage any foreign tourist to behave like homeless people in their host countries and plan their trips responsibly.

after researching transportation a bit, here's a revised version

14th:
train overnight (moonlight nagara)
get into fukuoka by the evening
15th:
Fukuoka
start train down to kirishima
sleep
16th
get into kirishima
sleep
17th
Hike Kirishima
get down to Kagoshima
sleep
18th-20th
ship over to
Yakushima
21st-22nd
ship up from yakushima, over to miyazaki
Miyazaki
Takachiho
Udo Shrine
train up to Beppu
sleep
23rd
Beppu
train back up to Fukuoka
train back to japan

aside from the moonlight kyushu, I believe there is public transportation to all the places (trains, buses) also hopefully i can hitch a ride once in a while.
I dont plan on seeing the whole prefecture of Miyazaki, main interest are Takchiho and Udo shrine.
Also, rental car/plane is not an option, I'm traveling by the Seishun 18, so it'll be train train train for the most part, the only really remote places are Kirishima (but hardly) and Yakushima, but even those are reachable by bus/ferry, so I'm sure train is more than enough to get to the places.
I did try to empty up the trip a bit more, to allow more time for moving between places (never knew it takes so long to get from Hakata to Kagoshima!) so hopefully that makes it a bit more easy going.

Even if you succeed making seat reservations for the Moonlight Nagara, note that you will be spending, you will be spending most of your trip (except your days in Yakushima) on board of local trains. If you wish to actually do some sightseeing, too, then I don't think that the Seishun 18 Kippu is the practical ticket for your trip.

And you need to look up train and bus timetables in Miyazaki in detail. It is not an good place to get around quickly by public transportation, especially if you are bound to local trains.

23rd
Beppu
train back up to Fukuoka
train back to japan

The trip from Beppu to Tokyo takes 24 hours, provided that you do not make a detour via Fukuoka (but change trains at Kokura Station, instead), there are no delays and succeed making seat reservations for the Moonlight Nagara.

Again, I recommend to think twice about doing the trip by Seishun 18 Kippu. Or at least study the timetables in more details.

I've had good experience with the Nagara and the Seishun 18, aside from the money issue, I chose the seishun so I have more flexibility stopping and going. No problem with taking local trains whatsoever. Also of course I will be looking up the train schedules in more detail (as well as bus) but I did find that from my earlier trips with the seishun 18 the local trains do give you a bit more flexibility.
As for reserving the Nagara, again I've done it before (in fact the Nagara was about half empty the two times I've been on it) also since I'm not a tourist I have flexibility to move the trip a day or two back and forth.
I'm more concerned about how much I can fit into one day, and as far as the itinerary seems viable for how much I'm seeing and moving about in a certain day, figuring out the specific train times/etc is no problem.

Also I guess I should add that the main reason I'm going on the trip is to go hiking in Yakushima.
Also from the looks of things, aside from the initial trip out to Kyushu, the only times I'll be on the train for the majority of the day will be going down to Kagoshima.

Do you think it'd be easier to travel I omitted either Beppu or Miyazaki?

What about taking a highway bus down from Fukuoka to Kagoshima?
http://www.jrkbus.co.jp/sakurajima.html

Is there also one between Miyazaki and Beppu?

okay here's one more revision of the itinerary, let me know if this seems a bit more doable.

14th:
train overnight (moonlight nagara)
get into fukuoka by the evening
sleep
15th:
Fukuoka
overnight bus to Kagoshima
16th
get into kirishima
hike kirishima
sleep
17th
down to Kagoshima
ferry over to Yakushima
sleep
18th-19th
hiking Yakushima
20th
ship up from yakushima, over to miyazaki
Aoshima
Udo Shrine
back to Miyajima
sleep
21nd
See Miyajima
train to Beppu
sleep
22rd
Beppu
train to Hiroshima
sleep
23rd
Hiroshima
train back to Tokyo

The new itinerary looks much better now. Still many days and nights spent on local trains, but much more doable than before.

From Kirishima, you could consider flying to Yakushima. The price difference to taking the ferry is probably relatively small, but you can save time, because the airport is just next to Kirishima.

On other sections, too, I recommend to consider a domestic flight. For example, Sky Net Asia has discount fares of around 11,000 yen one way on the Tokyo-Kagoshima and Tokyo-Miyazaki routes if booked far in advance. Likewise, offers discount tickets for under 10,000 yen on the Tokyo-Fukuoka route.

For example:

Tokyo - (train) - Fukuoka - (train) - Beppu - (train) - Miyazaki - (train) - Kagoshima - (ferry) - Yakushima - (air) - Kagoshima Airport - (bus) - Kirishima - (bus) - Kagoshima Airport - (air) - Tokyo

Just an idea... But your own itinerary looks okay too.

Money is an issue, so I don't think I'll be able to fly, I've decided to go with the bus down from Fukuoka since it covers one night of lodging as well.
As for going down to Yakushima, the jetfoil things get there in a couple hours, and the train is about an hour from Kirishima to the port, so I don't find it too bad a trip. Flying would cost just about double, which is unfortunately a bit too expensive and I am really trying to do this on a budget.
Thank you so much for the suggestions so far though, I see that I'm gonna be riding the train a lot, but I don't really mind, I see it all as a part of the trip and I've been okay with it in the past so..

Hello Peter(guest). I'm trying to plan a 10-day trip down to Kyushu around the same time as you planned yours last year. Thank you for the posting and the research you put into it. I was just wondering how it went - was it too packed in terms of what you intended to see? Was the timing right? Was it more expensive than anticipated? Was it super cold? I've only got 10 days and those go quick, especially when I want to see so much. But one area I would really like to go is Takachiho and Beppu and Kirishima and possibly Fukuoka if I can fit it in. Are there any places you would highly recommend?

Any advice you have about your trip down there would be greatly greatly appreciated. Thank you!