Here are my recommended places to visit in Japan!!
Tokyo:
Kaminarimon
Tokyo Skytree (online reservation recommended)
Team Lab (online reservation recommended)
Shibuya Scramble Crossing
Kyoto:
Kiyomizudera Temple (admission fee: cash only)
Fushimi inari
Yasaka Shrine
Ryoanji (admission fee: cash only)
Byodoin Temple (this place is also famous for Japanese tea)
Osaka:
Dotonbori
Osaka Castle
Fukuoka (work in progress)