I suggest itinerary after Kyoto. This itinerary is including links.please check.
Plan1
15 Kyoto
16 Kyoto City sightseeing
17 Fushimi Inari Shrine + Nara 1 day tour
18 Kyoto City sightseeing
19 Himeji 1 day tour and Kyoto City sightseeing
20 Hiroshima+Miyajima
Miyajima, an Island where People and Gods Live Together
http://www4.ocn.ne.jp/~miyayado/english.html
21 Fukuoka
22 Beppu 1 day tour
23 Nagasaki 1 day tour
24 Osaka.
25 Kobe One day tour (Trains from Kobe to Osaka are running frequently.you can enjoy Kobe night)
26 Mt Koya One day tour
Official website of K
http://www2.ocn.ne.jp/~koyasan/indexe.html
Koya-cho Lodging: Read Reviews and Compare Prices - TripAdvisor
27 Tokyo check in
28 Tokyo City sightseeing
29 back home
I know you definitely are not going to sleep in Osaka(I wonder why). But staying in Osaka is efficient for both of one day tour and going back to Tokyo.According to this plan,you don't need to repeat check in and check out.
Plan2
15～23 same as plan1
24 kobe
25 Kobe
26 Mt Koya
27 Tokyo check in
28 Tokyo City sightseeing
29 back home
You don`t need to stay Osaka.
Visiting Kobe and go to Mount Koya for the night is possible.But you will be from Fukuoka.I never recommend.
One day tour from Kobe is OK(Plan3).
About Onsen in Beppu
you can't use onsen in the hotel you referred to without staying night there.
There are municipal management Onsen.
Beppu City Official Web
Beppu Hot Springs
Your husband is so shy? Don't worry.there are also some sand bath in Beppu.
You don't need to be full nude.
And there are some privately‐operated Onsen which have family bath.
ADD NEW LINK
http://www17.ocn.ne.jp/~ftio/
8.Kitahama Hot Spring (Termas)
The open-air bath to go in with a bathing suit!
Holidays : Thursday
Nagasaki
About Nagasaki | Nagasaki City Tourism Guide Amazing Nagasaki
I can't say which city is better.At least, if you are from Netherlands or
interested in history of Christian in Japan,you might enjoy Nagasaki.
Ghibli museum
I recommended Shinjuku + Shibuya + Ghibli museum in Mitaka.Because of their locations.At least,walking from Odaiba to Mitaka is insane.Don't try.
To be honest,I think itinerary in big city like Tokyo is not so important except reserved ticket.You can easily get info there and Public Transportation is good enough.