Hey Ben, Seraphim here.
Advice:
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It is typhoon season, so it is slightly cooler then it has been for the last few months. However Typhoons happen very regularly. While I checked the weather and it looks fine, be aware that they can happen.
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GET AN UMBRELLA. Rain can be bad and when it happens it happens. Do not be without an umbrella. Good news is every convenience store sells them. But having one handy is a good idea.
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Convinience stores are you friends. Trust the food is fresh everyday and goo for a cheap snack. Convinience stores are worlds better then in NA. Also you can get cheap 2 L water bottles for the price of a regular water bottle that you would get from a vending machine. Convinience stores have tons of emergency stuff too.
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Google maps helps with finding your way on trains. Get a pocket wifi at the airport and use google maps. It will tell you the fastest and cheapest route to get where you need to go. Also a side note is that until you leave the gates at a train station it costs you nothing. So if you go the wrong way it only costs you time.
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Get an ioca card/transit card. They are reloadable and make it WAY easier then constantly buying tickets.
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Drink lots of fluid. Not just water but things with electrolytes. I saw someone say cc lemon, but piccori sweet too. Either way take some vitamins to stay healthy as Japan is hot and humid.
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Manners go a long way, learn important words to say thanks, sorry, and such. Japanese people are polite and expect you to be polite too.
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DONT TIP EVER
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Cash is king, bring lots of cash as everywhere takes cash, and don't be afraid to carry a fair amount as Japan is very safe. Japanese ATMS don't always take north America cards and have big charges for taking money. Japan can be expensive so keep a level head around purchases.
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BE POLITE
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Tokyo is very English orientated so don't be afraid you cannot speak the language.
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Never object to people with "well in my country..."
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The train system is your best friend, but remember service ends at midnight. Also it starts at 6 am
I will add more later