Rail ticket advice for family of 6 first time travellers in Japan

Hello - there is so much information regarding rail passes and tickets in Japan I am having trouble working out my best options.

The basis of our travel....
2 adults and 4 children aged 18, 12, 10 and 5 (obviously our 18yo will be considered an adult).
* Train travel from Narita Airport to Ueno Station Tokyo. * 9 days in Tokyo using public rail and buses. May include day trips to attractions outside of Tokyo. * High speed train from Tokyo to Kyoto. * 7 days in Kyoto using public rail and buses. May include day trips to attractions outside of Kyoto. * High speed or regular train from Kyoto to Osaka. * 2 days in Osaka using public rail and buses. Including rail transport to Osaka International Airport Itami.

From what I read a Japan Rail Pass is not good value for our situation because of our duration in Japan while not making a lot of long distance travel (only really the trip from Tokyo to Kyoto). I also understand that Tokyo and Kyoto/Osaka operate on different regional rail systems/operators (so there is not a common ticket across all 3 cities).

Any advice on the best and most economic rail options would be well appreciated, with 6 people in our family, prices add up very quickly....Kind Regards Muzza.