My sister and I have been to Japan/Tokyo Disney twice now, and we ABSOLUTELY love it.
Tips on the Tokyo Disney side of things:
1) If you're buying multi-day tickets, they MUST be consecutive (for example: Monday, Tuesday, Wednesday). Make sure to check out a crowd calendar. Generally, crowds are horrendous on the weekends. Plan all of your days on the weekdays! (But double check the crowd calendar to make sure).
2) Disneyland tips: you have to ride Pooh's Honey Hunt, and after that Monster's Inc. I would run to Monster's first thing in the morning to get a fastpass, and then get in line for Pooh ASAP. The rest of the day just be smart about always having a new fastpass lined up since they do the old-school paper system (so you can really capitalize if you're smart about it). The noodle shop (China Voyager) in adventureland had really good noodles, while the curry shop (Hungry Bear Cafe) has really good japanese curry. For a fun dessert, check out the alien mochi in the pizza restaurant in Tomorrowland (it also has a really....interesting video playing throughout the restaurant). You NEED to see their nighttime parade. Look up any festivals that may be going on during your trip, since they have a lot.
3) DisneySea tips: Mysterious Island is absolutely incredible (I loved both rides there). You probably want to prioritize fastpass for Journey to the Center of the Earth, but I also really loved 10,000 leagues, Indiana Jones, and Sinbad. The whole park looks great at night. Look up unique snacks and treats that you might be interested, although some are seasonal. We only ate at Vulcania, but it had a really unique atmosphere and good food. Also check out any festivals they might have, and look up the "lottery" system for reserving seats for some shows (same for Disneyland). We really enjoyed Big Band Beat (which requires a lottery, or going to the first showing). In general, you can easily walk to the Disneyland entrance while DisneySea requires a bus or monorail to get to (as far as I know). Also, fair warning: the monorail costs money in Tokyo Disney.
Tips on the Japan side of things:
1) Tokyo tips: check out the teamLab Borderless digital art museum in Odaiba. Incredible, incredible dynamic optical illusion art that you can interact and walk through. I really liked the Ueno region and park. There's an awesome bread shop near the train station that has all kinds of unique Japanese breads. Buy the Japan Rail Pass. You can use it on the Yamanote train line which goes through all of the major stops in Tokyo which will save you a LOT of money. You can also use the pass to go throughout the rest of Japan (such as to Kyoto), but make sure you know which train is applicable for the Rail Pass. Asakusa had a lot of good street food and an impressive shrine. At all of the shrines, you can buy a "Goshuin" prayer book which has blank pages. At each shrine, you can have the priests draw ink prayers (which are unique to each shrine) in a page, and collect them for the various shrines. Really awesome. Also, expect the trains to be PACKED during rush hour, ridiculously so. Just mentally prepare yourself. Akihabara is a place to go if you're into "anime" culture.
2) Kyoto. We didn't spend much time here, but definitely check out the street food street, Nishiki Market. Try out Takoyaki and any black sesame desserts.
3) Osaka. Also didn't spend much time here, but this is THE food capital of Japan. Check out Dontonbori street for incredible food and awesome building sculptures.
4) Nara. GO HERE. Seriously. The entire town is full of domestic deer that you can interact with. The deer near the city center can be aggressive, but if you go towards the forest, they're a lot calmer. Lots of great shrines and tourist places to visit. If you're up for it, I highly, highly recommend the Deer Park Inn (a "hostel" in the middle of the park). It has shared bathrooms and not the most luxurious living quarters, but it's extremely cheap and well-maintained. The people that run it speak English and are always incredibly friendly. You'll wake up in the middle of the park with deer outside your window. It's great.
Generally, Japanese people are incredibly polite and you should be polite with them too. They have a lot of strict and sometimes strange rules, but try to follow them. Sorry for the wall of text. I...really enjoyed Japan. Good luck!