Get a Suica card immediately (can buy from machine for ¥2000 (¥500 refundable deposit for the card, ¥1500 initial balance). This will make your transportation life much easier - otherwise you have to buy separate tickets for each subway line and it's confusing/terrible
Japan Post (the post office) has ATMs that work but they typically close/lock them up after 7PM or 9PM. Can dispense ¥1,000 or ¥10,000 bills
7-11s also have ATMs that work but they only dispense ¥10,000 bills.Breaking change is typically not a problem anywhere, but 7-11 won't make change for you unless you buy something.
There are some Citibanks as well.
Discover is cross-compatible w/ JCB and Union Pay rails and is actually quite useful in Asia.
If you travel a lot, Charles Schwab is awesome since they refund all ATM fees at the end of the month
In general, just try to be polite, my most useful word is sumimasen (means: please, excuse me, and sorry). my conversations usually go 'sumimasen, do you speak english' :) everyone says 'no' or 'a little' but in tokyo i haven't found basic communications to be too bad and everyone's super nice and tries to be helpful. google translate will help w/ the rest.
Ordering food is usually pretty simple since there are plastic food models and photos of everything. Also the machines aren't too hard to order from when those are there. Otherwise, showing a picture of what you want (taking a picture of a picture, or using a Tabelog/4SQ pic, etc etc works pretty well)
Some places, noodle shops most commonly, have ticket dispensers at the front which may not have pictures. If you have an Android the camera function in Google Translate is very useful for this. If all else fails just ask for "shoyu ramen negi chashu" (ramen in soy sauce broth served with pork and green onion) or "konbu udon" (udon in salt broth served with seaweed)
Japan is pretty much the safest country in the world. Just ignore the Nigerian (more annoying because they follow you and keep bugging you if you seem Gaijin/to understand English)/Yakuza (polite and oftentimes will point you to where you want to go) touts and you'll be fine.
SIM cards are a pain in the butt in Japan - basically you can't buy a prepaid regular SIM (you can get a data-only SIM though) - you can rent one, but data is like $15/day (Softbank SIM at airport) or you can get a data SIM (~$30+), but if you're sharing w/ people you can get a wifi hotspot for not much more and is probably more useful.
they sell a 1gb/30day data sim for like $40 and they will deliver to hotel or the airport for pickup (make sure it's during delivery desk open hours though if you do that) - there's free wifi in the airport btw
the no-registration pack is 30days/500MB and $40, but your only no-registration option once you're in the country
The pricing on the registration one is pretty good - $30 for SIM and then $10-20/mo. Requires registering w/ JP address. Comes with a free Wi2 wifi account that is extremely useful
There's wifi everywhere but almost all are paid services that require registration. A lot of the free hotspots email you a code to login. That doesn't help if you don't have internet to start with (in jp like all phones have email so i guess it makes sense, but it's still terrible)... JR stations have actual free wifi as does FreeSpot (very rare around town). Starbucks wi2 is free w/ registration.
Hunter BBe careful about which apps you use when you're on mobile data. Snapchat is a bandwidth hog if you're on Android because it uses a lot of background data. It's easy to slurp up data on Instagram too. FB messenger is great, but don't browse news feed too much. Just think about the media types; generally images = yellow light, video = red light.