Hi there!
That's a lot of interesting questions, especially since your trip is one that is somewhat unique.
At the same time I have to say that it really looks great, especially since in includes Kyushu and Okinawa.
Once you arrive at Narita Airport you've got two options. The first is the [Suica + N'EX] package. This includes a discounted ticket on the Narita Express to Tokyo and a pre-loaded suica card with 1500yen which you can use to travel around the capital and other parts of Japan.
The 2nd option is the [Keisei Skyliner and Metro Pass] this is a ticket on the Keisei Skyliner to Tokyo (Ueno) and also includes an all day metro pass.
The Keisei Skyliner pass may be a little more economic because you can travel as much on the Metro as you like for a day or two. However I usually recommend the Suica package because it is more flexible and the Narita Express stops at more major stations in Tokyo.
For general travel in Tokyo there are lots of options, one the all day metro pass and other is the Tokunai ticket which allows for unlimited travel on local JR lines in Tokyo for a single day. Here's a great website with all discount tickets listed in Tokyo it is hard to say which is best as it really comes down to what you would do with them.
I would recommend sticking to a Suica card if you are unsure, this because it is valid on every kind of transport and makes for very convenient travel (however it does not provide a discount by itself).
Looking at your travel after Tokyo it all is spaced apart so it can be hard to really take advantage of the JR Pass, be it a 7 14 or even 21 day pass. Maybe when you travel from Kyoto to Nagasaki (Point 9) a 7 day JR Pass could be useful. A normal ticket is ¥ 20,090 and the 7 day JR Pass is 28,300yen, so it would not be hard to making savings with it if you did some additional travel with it. You may want to look into a JR Kyushu pass for your local travel around Kyushu though. A 7 day JR Pass could also be useful for your last week. When you travel from Nagasaki - Kansai Airport (¥ 19,730) and Kansai Airport - Narita (Airport, I assume) (¥ 17,700). There's no direct train but the travel is pretty forward and mainly traveled with the Shinkansen, travel time is 4-5 hours.
On your way to Kyoto it looks easier to make a stop over at Matsumoto than Kanazawa, especially since you can take a direct there from Shinjuku (Tokyo). This would also be a more economic option. Once you are in Kyoto consider buying a 500yen bus ticket which is valid for a full day and allows for unlimited bus travel. This is especially great because a normal bus ride is 220yen. Unlike Tokyo, Kyoto is best traveled by bus making this ticket the best way to get around.
For local travel in Kyushu you have also two options, one is the Kyushu rail pass (mentioned before) there's bus pass, both are pretty good deals although I personally prefer the rail pass as rail travel is quicker and more comfortable.
Hope this helps you!
Daniel