I'm looking forward to Harijuku. I like girls things too.It might be hot then, check the weather.
Also, I wouldn´t pack too many destinations to see in that time, you want to enjoy each place, especially if your son has anxiety.
I stayed in a Ryokan in Kyoto. I think I found it on booking.com
Kyoto is very peaceful, some temples are crowded but some are more quiet...I love the japanese gardens.
You can get around with speaking (basic) english. People are so respectful and polite and rules oriented that even crowds didn´t feel stressful to me.
I only did Tokyo, Kyoto, Osaka. But thats because it was my first time solo traveling, I wanted to soak in the lifestyle of Tokyo and went to Sanrio Puroland (I´m a Hello Kitty lover!)...also pet cafés, the Robot restaurant which puts on a crazy show of japanese 80s kitsch, went to Studio Ghibli museum (if you like animé) I could be fully geeking out on toys and kawaii things and no one blinks an eye there lol.
Book your rail pass before going.
I loved it so much that I want to go back...But South Korea caught my eye haha
The Robot restaurant is on my list for Tokyo. It sounds fun!
I'm torn on owl cafes. I know my son would enjoy it, but is it ethical. Cat cafes seem ethical because they are domesticated animals. I'm seriously allergic to cats though.
I've already looked into the rail pass. That's my plan for getting around.