Rather than Tokyo Disney, I would do a day trip to Nikko and Kegon Falls (in the same town)
https://www.youtube.com/watch?v=QPoapIWnl04
https://www.youtube.com/watch?v=1sA86NBzEV4
Bullet train to Kyoto is a fun hassle free way to travel between Kyoto and Tokyo. Kyoto is all about the palaces and shrines. The two palaces on the outskirts of town are particularly notable, but Kyoto is just filled with quintessentially Japanese gardens and shrines. Like this one – the famous zen garden:
https://www.youtube.com/watch?v=-2uLwcLJTaU
This one is located near the Golden Pavillion, another popular (for good reason) Kyoto landmark.
Tokyo is so big, it is best done by picking “neighborhoods” or sections. For example, Shinjuku/Harajuku are one or two subway train stops apart. For young adults, the park at the Harajuku train station is a hot spot and a short walk to the Meiji Shrine. So, that’s a whole day in one “neighborhood”.
Ginza at night. Definitely Ginza at night. The people watching (and neon) is terrific. To me, the essence of Tokyo is the hustle and bustle. It’s just insane. The main Imperial Palace is in this “neighborhood” so that might be another day (and evening).
The two times I’ve been to Japan, I’ve gotten around on the subways and trains. Get the JNR rail pass mentioned above. That will get you anywhere you would want to go.