Figure out where you want to be generally then, outside a handful of "must-sees" for you, have fun getting lost and exploring. Your iPhone is all you really need as it does everything you want from navigating by rail (we did do a 3rd party app as it was super easy to use underground when cell service/wifi wasn't available or weak) to figuring stuff out.
We did a week in the city and a week doing Kyoto and travels there. It's easy to do many weeks in Tokyo and a few days in Kyoto we decided.
Eat as much as you possibly can and without pretense. Eating/dining was our primary goal along with exploring and you'd be amazed at how amazing food can be everywhere from a 7-11 to world class restaurants and everything in-between. My wife, through a series of international phone calls to maître-d's and slight fibs, got us into Le Chateau Joel Robuchon for New Years Eve dinner where it was every bit of three Michelin stars and a mortgage payment but it is also a dinner that I will remember forever. Higashi-Yama in Meguro
https://higashiyama-tokyo.jp/ was incredible omakase Japanese in an intimate setting. Eat at the bar as they prepare everything in front of you.
Stop by the old market surrounding Tsukiji Fish Market that is still going (do fresh sushi breakfast there) even though the auction market itself moved to the new Toyosu Fish Market which I believe you can still view (from designated viewing area above) the tuna auctions.
Grab a cocktail at the New York Bar at the Park Hyatt at night and take in the lights. Actually, get anywhere up high at night and marvel at how fucking vast the city is. (and how clean it is)
Everyone is kind to a fault, so we found sumimasen to be our most used word in case we were offending anyone unintentionally or thanking them.
Train-walk-explore, repeat.
Very jealous, I can't wait to get back.
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