@Sn0wscary8
Me too - that's what I did the first few times I came, planned my own.
The first time I really didn't speak much Japanese at all, but managed it because I planned everything so well.
That said, of course it's great to take a phrase book with you for emergencies and even if you only know "arigatou gozaimasu" (thank you), Japanese people are always incredible happy and touched that you said anything at all.
I would definitely allow one or two days to enjoy Kyoto - I still need to go back. It has some beautiful shrines, I love the Arashiyama bamboo forest also. Maybe even three so you can enjoy everything rather than rush.
You may enjoy Ise Grand Shrine too - I really enjoyed it, it was beautiful and lots of street food to enjoy.
For sit and watch the world go by there is a Starbucks (bear with me) that overlooks the Shibuya crossing in Tokyo, amazing for just watching Japan "happen".
In Tokyo there are lots of themed cafes (actually everywhere but easy to find there) and the Ghibli museum if you've seen any of the movies.
For the first time, especially with the time you've suggested I would definitely fit in Tokyo (lots of different areas to enjoy although it is very busy) Kyoto, Nara (has a deer park where the deer are very used to people, you can feed them and pet them. They do sometimes bite bums I've heard but they were fine when I saw them.)
Also a wonderful village called Takayama, I've never been there but sent my parents off there on a day trip when they visited and they thought it was amazing.
Hokkaido is on my must-go list - they have a snow festival in the winter and generally looks amazing.
Kobe is also supposed to be great - it's on our short-honeymoon shortlist.
The Shinkansen is very expensive so I'd recommend looking into the Japan Rail Pass - you can use the Shinkansen loads and JR operated trains. It looks expensive at first but once you've used it just twice - it's worth it.
For fun but not so cultural trips there is USJ (universal studios Japan) and the Harry Potter area is fantastic! I loved it.
If you want to stick to a budget I recommend the Toyoko inn chain - it's kind of like Japan's Travelodge - but always very clean and comfortable.
You can also try the traditional Japanese ryokan - although I liked beds haha.
Make sure to avoid Golden Week in May - it's a long national holiday and really busy and crazy everywhere you go. Also Summer gets unbearably hot (I think they were reporting in the UK last year) so try to avoid July/August/early September if possible. However with DCs that may be difficult - July is still tolerable but my goodness August.....last year got up to 42/43 degrees daily, and it didn't go down much at night.