I am glad that you are interested in Japan!
I have an old friend in Japan, and he always takes me to subcultural places! Then I found out that Japan has so much that foreign people don’t know about. For example, every shrine has its original history, and going to a shrine means a lot to Japanese people. Shibuya & Harajuku have so many fashionable backstreets to explore. I always have good experiences in Japan, and it is because I luckily have him as local friend.
I told my friend who was going to Japan for a trip. He found a service that matches locals and travelers to be friends. I would highly recommend this website! https://goo.gl/uDGnlU
I think you will find someone that can help you have local rich experiences in Japan.
Perhaps you can browse Atlas Obscura, which has a variety of unusual places to visit: http://www.atlasobscura.com/things-to-do/japan
If you are planning to go somewhere specific, or at a specific time try to post again. There are many interesting local festivals but they only happen on particular days of the year.