A few pieces of advice.
1) Rent one of those pocket Wifi things. They'll deliver it to your hotel for you and it allows you to use your phone via the pocket wifi device. They didn't cost much last time I was there and you just drop it in the mail at the hotel when you are done.
2) Get a translator app (unless you'll have a person with you that speaks both languages)
3)There are a couple of Tokyo subway apps. Get them on your phone before you go. Figuring out the subways/trains without someone who spoke Japanese was not easy, but those apps helped.
4) Don't cross the road when sign turns red. The cars assume everyone will be out of the road.
nowadays, i would recommend getting an esim over a pocket wifi (use an app like ubigi)
also google maps should be more than sufficient for navigating the subways, and google translate does a pretty good job for simple communication (and you can use your camera to translate signs/menus)
japan is having a shortage of IC cards (i.e suica/pasmo) right now, but you may be able to get one if you fly in outside of tokyo or get a temporary 30 day version if you are flying in through haneda/narita. having these is a lifesaver for the trains, busses, etc and it also works at the convenience stores/vending machines which are everywhere. if you have an iphone, you can create a digital IC card now in your apple wallet and preload it. if you use android, you are out of luck (unless you have a japanese market android phone).
everything we ate in japan was amazing and the prices were pretty cheap in general relative to what you see in america. don't sleep on the convenience store food either.
tsukiji market is great if you want to eat a lot of different things. we did breakfast/lunch there one day.
if you are into nerd stuff (not only anime - video games, tcgs, etc.), akihabara is cool for shopping. some of the shops like super potato are almost more like museums of old video game stuff. if you aren't into nerd stuff, there are other areas that are also good for shopping. there are so many malls/department stores all over you can almost just pick one at random and find cool stuff. hands shibuya is their flagship store and was full of stationary/craft stuff that made for great christmas gift shopping. there are secondhand/thrift stores all over too where you can get some pretty crazy deals.
some things require reservations, you should be able to go ahead and book those now if you are interested. some examples are teamlab planets (kind of cool, but missable), shibuya sky observation deck (if you want to go up top around sunset, alternatively there are free observation decks in shinjuku at the tokyo metropolitan goverment buildings).
i did the planning for a group of 6 of us earlier this year, so happy to answer any follow-up questions