As is, your itinerary and schedule will cost you - but if you are willing to expand your plans a bit, you could make a 14 day JR Pass pay off very handsomely.
Two weeks in Tokyo in more than excessive. You could get a 14 day JR Pass and use it to go to several day trips in the area - Nikko, Karuizawa, Kamakura, Kusatsu, Izu and Hakone are some possibilities (for Hakone, a Hakone Free Pass would also really help) as well as while in Kansai taking the bullet train to see Himeji Castle (the nation's finest). That, with your regular plans, would easily make your pass pay off.
For returning back from Nagasaki to Tokyo, if you want to save your time, money and sanity, the ANA Experience Japan Fare is one way. But if you have a lot of stuff and don't want to pay the excess baggage charge, two other possibilities are the Star Alliance Japan Airpass (if you are flying to Japan on a Star Alliance carrier) or the JAL Yokoso Air Pass (if you are flying on a One World carrier). Both are conjunction tickets and would follow your international carrier's baggage limits - so unless you are already bringing an excessive amount, you could get by with no charges.
http://www.ana.co.jp/wws/us/e/wws_common/book-plan/fare/special/airpas...http://www.jal.co.jp/yokosojapan/Nagasaki is really the most interesting city on Kyushu and there are many places to see - but for a week you could easily branch out and see nearby areas like Huis Ten Bosch, Unzen, Shimabara, and Hirado, plus cruise the islands.
You can see a lot of the best in Nagasaki at
https://www.youtube.com/playlist?list=PL7LcPcmoSg-gbw2yXNLK92siHyNqSNx...For your other week you didn't mention anything, but it is easy to travel around on a Kyushu or Northern Kyushu Rail Pass and save money.
Fukuoka has a number of good places to see.
http://www.thejapanfaq.com/fukpic.htmlespecially the Nanzoin Temple which is a must-see place.
https://www.youtube.com/watch?v=lT4VQFmHFyMBeppu and Yufuin are both famous for hot springs, although Beppu also has some other tourist attractions, like its Hells Tour and nearby monkey park.
https://www.youtube.com/playlist?list=PL7LcPcmoSg-hOggZamc2lUNTr46ApKX...Kurokawa is perhaps the best hot spring place on the island though, however you can't get there by rail. Kumakoto has a number of good places as well, such as its castle, Suizenji Garden, and Mt. Aso (although the crater area is currently closed).
https://www.youtube.com/watch?v=K9xyXmU8U1gIf you want to go farther south, Kagoshima also offers a number of good places, and it is easily accessed by bullet train. Sakurajima is the pièce de résistance, and if you like some hiking the area has some very good places.
https://www.youtube.com/playlist?list=PL7LcPcmoSg-irtXXB8IJMdkB9mF0qjn...It should not be hard to fill up your time with some very nice places and memories.
