There are some great tips in the forum especially the last post by Tracy. I'll try not to duplicate but will add to it. First, she's right - get a mobile hot spot. There are few if any English street signs and it is enormously helpful to use google maps when lost or looking for things. Second, as soon as you think you're confused - get help. The Japanese people were some of the most friendly and helpful people I've ever encountered traveling. People often came up to us to ask if they could help if we were looking at train maps or schedules for example.
Trains are always on time and immaculate. Get a train pass if you plan to do any touring beyond Tokyo. Get a Pasmo or Suiza pass for the local Tokyo trains - basically you can top it up whenever needed and you don't need to find change or buy tickets for each leg of your journey.
Skip a lot of the big 'tourist' sites - many are highly commercial and not worth it. If you are traveling beyond Tokyo - say to Kyoto or Kanazawa or other historical cities - you might want to skip most of the temples and shrines because you'll find just as nice ones and many more to choose from in those places. What I'd recommend instead is getting out into the small neighborhoods of Tokyo - away from the big commercial stuff. We found a number of lovely places: Daikanyama, Naka Meguro, and Shimo Kitazawa to name just a few. There are some articles you can google about others. In each of these, we found great neighborhood shops, cafes, bars, etc. along with a special vibe and principally local people. Daikanyama is the most developed and has a must-see: T-Site - several buildings - anchored by Tsutaya's flagship bookstore (more than a bookstore!), and a cafe and restaurant. the architecture is amazing but also the bookstore carries topical gifts, music and art and has a gorgeous bar/cafe in one building that is worth a rest stop and a beer if not some food. Totally unique experience.
Naka Meguro is along a tree-lined canal and has tiny little restaurants, shops and galleries and is peaceful and a lovely walk. You really can enjoy how the hipsters of Tokyo live. They have a baby cafe there where mothers come to have tea and let their babies play together for example.
Finally, I'd say not to follow most of the recommended restaurants except perhaps for a really good sushi meal. It is worth experiencing. Otherwise, stick to the Izakaya's and casual neighborhood places. We had a great meal one day in the train station when we were starved and tired and we totally surprised by the quality. Experiment, stop in and be friendly and you'll meet people and have a great time.
And oh, yes. Distances are huge in Tokyo so when something looks like it is a short distance - it will be further than you think. We walked on average 6 hours a day and our feet were tired. Do wear comfortable shoes and bring ones that can handle the rain - it really pours. I don't personally recommend crocs - I think they look ridiculous on anyone over the age of 5 - but that aside, it is terribly humid (or later very cold) so plastic shoes are not a good idea. BTW, the Tokyo-ites dress very stylishly and carefully, even men, so do be prepared to be respectfully dressed when you go to restaurants, etc. and especially visiting shrines and temples.
Finally, I do recommend getting out of Tokyo and seeing more of the country. Once you are in Japan, it is seriously easy. The Shinkansen (fast train) is amazing and you can be in Kyoto in 1 1/2 hours. Kyoto is well worth your time - 3,000 temples - great food, lovely people, and great shopping along of course with museums and amazing gardens! I also recommend getting out to the countryside and at least one small town - it is really beautiful.