I just came back from my solo trip to Tokyo and Sendai. I went for two weeks from November 22 to December 5. Seems you have a lot of ideas about destinations so I won't add more. But here are some observations I made while travelling solo:
1. Travelling is easy as all train stations and train lines have english names. Buses are a bit iffy as bus routes might not display stops in english, so its hard to know where you are going. In Kyoto buses are the only way to go and they are the exception. They have english names to their stops so you generally know where you are going. Here is some info on Kyoto bus network
http://www.insidekyoto.com/kyoto-buses 2. Bring your smartphone as Google Translator was my best friend. I have used it many times and they seem to understand what I am asking.
3. I ate solo all the time and there is no problem doing it. Most restaurants have bar seating specifically for solo diners, so don't feel embarrassed to eat alone. The only difficult thing is ordering. Especially in smaller towns, many restaurants do not have english speaking staff or english menu. What I did often was look for places with the food displays, take a photo of what I want, then show it to the server. Or, go to ramen shops with the vending machines. A huge tip is choose the button on the upper left hand corner. That dish is the "chef special" and is often the safest item in the menu.
4. Ramen is typically 600-900 yen, and soba is typically 500-800 yen. I found it cheaper in smaller cities than Tokyo. Ichiran (the ramen shop with solo booths) is actually pretty expensive. Once you pack the meats, garlic, and egg, each bowl is over 1000 yen. I recommend the mom and pop ramen shops as they are cheaper and less rowdy.
5. If you have some money to spend you have to get the wifi box. It allows you constant internet access wherever you go, even underground (though not in the mountainous areas). I found that I need it not only for social media, but also access google maps when you get lost. Also, I believe you need internet for Google Translate. I would not necessarily trust the free wifi because you have to register all the time and they are not always found everywhere.
6. Japan is one of the safest countries in the world and throughout the entire trip I in no way felt unsafe or endangered. Obviously you would avoid places you logically wouldn't go to, but I didn't feel threatened even in a dimly lit street.
7. Bring lots of cash. Most restaurants do not accept credit card, and even many stores do not accept credit card. I was in a department store in Kawagoe and even there I had to use cash.
8. In terms of passes, JR is not the only option. Local and private rail companies often have their own passes. I.e. the Kansai Thru Pass and Kyoto Bus and Subway Pass. Explore these options as I find JR can be more expensive than other transit systems.
Hope this helps. Honestly if there is one country to travel solo, its Japan. It's safe, people are generally friendly (or at least they keep to themselves), and the food and culture is amazing.
