Questions: travelling to Kyoto, Nara etc

Hello, I have yet another question. This time it is not about girls but about my actual vacation.

I will go to Japan next month from July 8th until July 25th. The first 7 days will be spend in Tokyo save for 1 day during which I want to see Mt. Fuji. The second week to 8 days I will travel around a bit. So I have some questions about this.
- The only place of which I am 100% certain I will visit it is Kyoto. I want to spend 2 days here and maybe travel from here to Nara while I keep my base there a third day. A few questions about this:

1. Should I take the Shinkansen from Tokyo to Kyoto since it is the fastest way to go?
2. What about a night bus/train to Kyoto? My Japanese friend told me it is much cheaper. But is it also safe? In Holland I wouldn't think about taking the train at night :p
3. Is there an easy connection between Kyoto and Nara?

Next, I have a few idea's about places I want to visit as well. But they lie far away from the area of Kyoto and Tokyo. They are:
4. Mount Koya. I have seen some beautiful images of this place. It would be an amazing trip. Is it worth taking and, if so, how do I get there?
5. Hiroshima. This has always been a place of interest to me. But I had always imagined it as being closer to Tokyo. There are also a few places around Hiroshima that sound interesting. So, should I make this trip?

I would like to know what you think about these idea's. If you think I should spend my time more efficiently and stay in the area around Kyoto and Tokyo then I would like to hear some tips of places to visit.

Money will be not so much the issue. I will have a budget of a few thousand Euro's to spend only on myself. And since I will have a free shelter for the first week I save a ton of money to spend in just 1 week.

Alright folks. I hope to hear from you :)

I have never taken the night train, but I have taken night buses dozens of times, and I can assure you they are perfectly safe - and cheap. However, they are NOT comfortable. Don't expect to get much sleep! If you can afford to, the Shinkansen will be a lot more relaxing.

There are plenty of trains from Kyoto station to Nara throughout the day. You should have no trouble.

Mt. Koya is definitely worth the trip! You should stay a night there in one of the temple lodgings. It is an amazing experience! Access to it is described here:

http://www.japan-guide.com/e/e4904.html

I do think if you have the time, you should include Hiroshima. The Peace Park and Miyajima are worth seeing.

A good sample itinerary is here.
http://www.japan-guide.com/e/e2400_tokyo_16.html
You can allocate more days in Tokyo by omitting Takayama and Kanazawa.

The answers to your questions are
1.2. depends on personal preference.
3.4.5 Yes.

Are you going back to Tokyo after visiting Kyoto, Hiroshima etc.? if so buy a 7days JR pass. it is less that a return trip from Hiroshima to Tokyo. You could go from Tokyo to Hiroshima in the morning of day 1. See Hiroshima peace park and a bit of the city in the afternoon. see Miyajima island the next morning, up to 2 pm, then go to Kyoto. (going to Miyajima and back by JR train and ferry is free with your JR pass. Visit Kyoto for a couple of days, visit Nara (JR train). Go from Kyoto to Osaka-Namba by JR trains then in Namba get a nankai sabic pass to go to go to Koya san. stay the night there and the next day by noon go back to Namba then take JR trains to Shin-Osaka and go back to Tokyo, on the 7th day of your pass. for details of trains check A-Z at the very top of this site (in A-Z . check transportation then trains then travelling to the towns cited above). for schedules check www.hyperdia.com be sure to read the help section first.!

Thanks for the answers. Indeed, it might be a good idea to buy a JR pass for 7 days. Does it mean that once I have paid for this I can travel unlimited for 7 days?

And yes, I will be returning to Tokyo the last two days to spend some more time with my friend and to be close to Narita where I have to take my flight back to Amsterdam.

After reading all this it seems that Mt. Koya and Hiroshima are really worth visiting. It seems like an expensive journey but I don't very often get the chance to go to Japan so I have to make it worthwhile right?

@ Ts, thank you for the link and the extra options in the area.

@ T (are you the same person as Ts?), I will look into Mt. Koya a bit more. Perhaps I could spend a night there. It sounds like an awesome experience.

@ Red Frog, thanks for the suggestions. I haven't thought about my travel like this before. I had in mind to go from Tokyo to Kyoto and then move along southward. If I make my trip as such I will a lot more in the south at the time of the big eclipse. That would be a nice bonus.

If anyone has more suggestions, feel free to speak up!

re JR PASS: http://www.japanrailpass.net/eng/en001.html
be sure to read ALL the pages..You must buy a voucher for the pass in your home country then exchange it for a real pass once in Japan at any good sized JR station. You can do the exchange in advance, on arrival or a couple days later and tell them that the pass should start on ...several days later. For long trips you should reserve seats in advance (I have done it the day before or a few hours before..). on short trips on local trains just hop on. You have to show your pass at a manned booth in the station going in and going out. The only restriction is that you can't use the Nozomi (fastest) shinkansen, only the Hikari (only a bit slower) and the Kodoma (slowest). and yes during these 7 days you can use the JR trains as often as you want. . .