Have you confirmed that you cannot choose Kansai Airport [KIX]?
My estimation of your cost on Tokyo -- Kyoto -- Osaka -- Nara round-trip rides and the three tips in Kansai Region is shown below.
You already have many destinations in Kyoto and in Osaka.
Depending on your | your husbandfs | your sonfs interests, maybe you add some sites.
It sounds better
not to cut one day for Kansai Region just to make use of a slightly cost-saving option.
When you do so,
in other words, when you get from and back to Tokyo in 7 calendar days,
the JTB JAPANiCan Tokyo -- Kyoto round-trip package sounds suitable for you and your husband (each).
There seems to be no child-rate version of this package.
https://www.japanican.com/en/tour/detail/PAS1J02031MKC/For your 11-year-old-son,
the price of the child 7-day Ordinary-Class Japan Rail pass
is about the same as the total JR regular cost (#);
however,
the above package is for Shinkansen Nozomi train rides,
which are not allowed by the Japan Rail Pass.
Therefore, when you take this package, traveling by JR regular tickets seems best for your son.
(#) Strictly, the price of the JRP is a little higher in Japanese yen, and you have to pay also a handling charge to get the Exchange Vouchers; you pay all the amount for the passes in your currency.
-- Estimation of the cost on your trips (other than Tokyo trips) --
The child-rate prices apply to your 11-year-old son.
[Conditions]
Traveling from Tokyo via Kyoto and Osaka to Nara then back to Tokyo,
within 10 calendar days.
Staying near Kyoto Station then near Osaka Station.
[Cost: JR regular tickets + non-JR passes]
Total cost
: 31460 yen per adult
/ 15620 yen per child.
Total JR regular cost
: 28060 yen per adult
(or 27020 yen when you do without seat reservation)
/ 14020 yen per child
(or 13500 yen).
JR regular fees in detail
: 17280 yen / 8640 as JR basic fare
(after 10 percent long-distance round-trip discount)
for Tokyo -- Kyoto -- Shin-Osaka -- Osaka -- Nara round trip within 10 calendar days.
: 5390 yen / 2690 yen
as JR Shinkansen Hikari surcharge, with your seat reserved,
for Tokyo | Shinagawa -- Kyoto (on the 24th of February 2019).
: 5390 yen / 2690 yen
as JR Shinkansen Hikari surcharge, with your seat reserved,
for Shin-Osaka -- Shinagawa | Tokyo (by the 20th in March).
NOTE
: When you do without seat reservation,
the price of the Shinkansen surcharge
is lower than the above
by 520 yen per adult / 260 yen per child,
regardless of whether you choose Nozomi or Hikari.
Total non-JR cost
: 3400 yen per adult
/ 1600 yen per child.
Non-JR cost in detail
: 900 yen on Kyoto 1-day Subway & Bus pass
/ 450 yen per child.
: 600 yen on Kyoto 1-day Bus pass
/ 300 yen per child.
: 800 yen on Osaka Metro 1-day pass "Enjoy Eco Card" for weekdays
/ 300 yen per child.
: 600 yen on Osaka Metro 1-day pass "Enjoy Eco Card"
for weekends and holidays (to be used on the 9th of March)
/ 300 yen per child.
: 500 yen on Nara Kotsu 1-day Nara Park - Nishinokyo Pass
/ 250 yen per child.