First Japan visit - rail questions

Hi,

First time traveller to Japan. Will be going with a 7 year old so I’m trying to find the best way to get around easily.

My itinerary will be
KIX - Kyoto 3 nights
Kyoto -Osaka 6 nights will do (Nara out of Osaka)
Osaka - Joetsu 4 nights (Lotte Arai)
Joetsu - Tokyo

While in Tokyo I want to visit Yokohama

What would you suggest in passes etc. I read JR pass is going up 70%!!