Utilizing Japan Trip with 7 day JR Pass & Other Pass to see most of Japan

I am in deep overwhelmed on how do plan our family trip in Japan. We visited Japan last August 2018 in Osaka/Kyoto/Kobe/Kochi but didnt see much of the places.  It will be my husband and my 2 young children ages 8 and 5 yrs old. 

We only saw Namba Glico Man area in Osaka in Kyoto we only been in Bamboo forest. 

This April 2019 we are staying in AirBnB in Osaka (Temma area)  from April 13th to April 19th then another AirBnb in Kyoto (South Fushimi-Ku area) from Aptil 19th till 24th. Our last stop is in Tokyo where our AirBnb stay from April 24th till April 29th in Asakusa area. 

My plan was to see more of these places below and on our own as much as possible with little tours maybe. 

Osaka for 3 days -

Kyoto for 3 days - 

Then 1 day trip to Wakayama / Mt Koya, Himeji, Hiroshima, Nara, Naruto or Mie area until we head to Tokyo area. 

I am planning to buy a JR pass - 7 days for all of us and we want to utilized this pass to go to these places. 

Also any recommendation to see the famous and how to utlized my JR pass or should I buy different kinds of Pass like Kansai Pass, Suica, Icoco pass? 

Hope anyone can assist me on this trip. Thank you very much