A few comments:

Arashiyama isn't that close to Kinkakuji. If you are taking a cab, then it is not as big a deal.

An 8 year-old might get "templed out" quickly in Kyoto (not knowing him, of course). If I were taking an 8 year-old there, I'd focus on a few very different temples/shrines, spread them out, and then try to do other things. Arashiyama works well for this (monkey park is great), so you are on the right track. You might want to do a "samurai/maiko" photo-shoot (not knowing your gender) with your son, the dress-up can be fun for both. Not sure what else to do in Kyoto for an 8 year-old, to be honest.

For Tokyo, Edo-Tokyo-museum is spot on. I'd also look at walking around Ginza for funky architecture and stopping in the Sony showcase building, and also a stop in Akihabara before or after the Edo-Tokyo Museum. If he is a fan of Miyazaki films, consider the Ghibli Museum, but make sure to book in advance. Also, do karaoke in a booth for an hour at some point.