Travel Check-Up and Review

This April, we (2 people) will be traveling Japan beginning and ending at Narita Airport. Our plan is to travel southbound for 2 weeks (April 9 - April 24). I would like to get your advise for the following travel plans.
We arrive to Narita Airport on April 9 at 16:45. We plan on getting the 14-day JR Pass. Since we want to be able to use the JR Pass until the very end of our trip and take the Narita Express getting back to the airport, we won't be able to activate the JR Pass until April 10.
When we land, we will take the 1000 yen bus to Tokyo.
(1) We stay in Tokyo from April 9 to April 11 (2 nights). (2) On April 11, we go to Otsu and stay from April 11 to April 13 (2 nights). While at Otsu, we plan to go to Kyoto for one of the days. (3) On April 13, we go to Fukuoka and stay from April 13 to April 16 (3 nights). (4) On April 16, we go to Kumamoto and stay from April 16 to April 18 (2 nights). (5) On April 18, we go to Beppu and stay from April 18 to April 20 (2 nights). (6) On April 20, we go to Okayama and stay from April 20 to April 22 (2 nights). (7) On April 22, we go to Kamakura and stay from April 22 to April 24 (2 nights). (8) Finally, on April 24, Kamakura to Tokyo and take the Narita Express back to the airport.