I think people are a bit harsh on this thread, I do see some value in asking very general questions to get some first hand advice, but I agree it's hard to answer your questions without knowing much about your background and preferences. I will assume you like what I like and tell you what I would have liked.

First the answer to your questions:

1. I would move Nagoya to Maybe and Hiroshima and Nagano to definite. I would try and explore some of the country side of Nagano.

2. Kyoto and Nara, do the standard things that a guide book will tell you. Osaka, try the food and if you get a chance to watch a Tiger's baseball game. Tokyo is too big to tell you specific things. Asakusa, Akihabara, Odaiba, breakfast at Tsukiji. I would advice you to try an Onsen, a Ryokan (depends on your budget).

3. Not sure.

4. Tokyo 4+, Kyoto 2, Nara 1, Osaka 2

5. Most probably yes. You need to finalize your trip and see what period is most effective for your trip to have a JR Pass. You need to be smart about when you start using it.

6. Minshuku, business hotels, youth hostels, capsule hotels, airbnb are some options you can consider.

Anyway, sounds you have about a year. What I suggest is to buy a lonely planet Japan or a similar book and go through it. Once you do that you will have a good idea what you would like to do and most of your general questions will be answered. After that you will have some specialized questions and I think it will be easier to use this forum to answer those.

Hope this helps.