ATM: If you had a CITIBANK account, then yes, ATMing money was a cinch. Not so simple for other domestic-USA banks. Citibank in Japan imploded over an accounting scandal a couple of years ago, so I doubt they’re still there–at least under the Citibank name. Your best bet today is probably to cash-advance from a (non-debit) credit card, or travelers cheques. I would usually exchange at the post office. No idea if things have changed. 15 years ago, a curious form of arbitrage happened over the fact that the exchange rates posted at the banks and at the post offices were updated at different times (an hour apart). You could convert a bunch of dollars to yen, make a mad dash to the bank, and exchange the yen back into USD for a profit. Run back to the post office, exchange…and so on til the hour was up. I knew a few folks back then that practically did this for a living. No idea if it still is going on today. Back then, the post office gave your the fairest exchange rate for dollars to yen.

Transportation: OK, you have the JR pass. Cool. Most useful thing you have besides the passport. As you already have noticed, you should get the underground pass, too. Eventually I had to start paying standard fares once I had a work visa–$115 per shinkansen run down to Osaka (and another $115 back) is no fun, although for commuters the “repeater” ticket was nice.

Speaking of transportation, get out of the city and up into the mountains whenever possible. A favorite weekend of mine would be a shinkansen/rapid trip up to Nikko, then up into the mountains to one of the hot springs resorts. These places were typically Y9800/night but were very nice resorts. Take the bus up to the lake along a switchback route, look down the side of the mountain, and marvel at how the bus driver manages to drive that route. ;) Might as well see the Tokugawa shrine, too. Escapes into the mountains were particularly nice during the rainy season as the sea level climate is just wretched.

Food: revelation #1: you can actually live off the food at their conbenis. This was pretty much my diet for the first three months, until I’d sorted out what places I liked (in Higashi-Nakano, then later Saitama). That, and Mosburger fries. Once I’d tried the recommended places, I had a short list of favorites for sushi, steak, ramen, udon and the like. A pity I can’t remember the names now. Except for one bar in Higashi-Nakano: “Old Crow.” Since it was my nickname already, I just had to frequent the place. It was some sort of english-basement type pub.

Revelation #2: McD’s in Japan still used beef fat for their apple pies and fries. Eventually I cut out the fries alltogether, but I probably represent 10% ofthe GNP on apple pies while there. ;) Revelation 2.5: KFC there had these rice curry balls with chicken in the middle. They need to have such things in the states!

Of course everything in Japan can be had out of a vending machine, although for some reason the number of Dydo machines in the greater Tokyo area that sold pink grapefruit juice could be counted on one hand.
On occasion you would encounter some ‘biergarten’ that would pop up on park grounds. Most of these were 1) cheap 2) excellent food. The beer was OK, I guess, but then I don’t drink beer, I drink Guinness. ;)

Shopping for loot: I have this little paperback book, “The otaku shopping guide” I bought in 1992 or so, back when LDs were your video media of choice. I’d buy LDs, box sets, manga, whatnot and ship the stuff via EMS back to the states. The guide had all the usual places: Mandarake, Animate, Pony Toy (gone now, I think), Liberte and other shops in Akihabara..etc. I usually rolled a loot foray for electronic gadgets and anime stuff into one trip per month as getting the stuff back to the house was a general PITA. It is probably all changed now, but one could get off the Yamanote-sen at Akibahara, duck in the Ghibli store there in the station, go down to the street level and have some decent curry in a shop under the tracks, then delve into the catacombs hunting for parts. (Note: always buy the light stuff first!) Then it was time to head down the street and into the anime shops with the occasional look into various tech stores.
This tended to take several hours. Make sure you’re prepared for most everything to promptly close at 7PM. A stop at the coffee shop above the catacombs for some caffiene, then onto the train with (by the end of my stay, I was using an aluminum flight case on wheels!) the goods.

I wonder if taxis are still as hard to find now as it was then. Those, and public trashcans. Oh, and if the public restrooms that commonly feature ‘slipper’ toilets are too much of a hassle, just find a handicapped stall. Although, the restaurants seemed to favor the western toilet.

OK, I’ve typed too long…it is just I can write for hours on this stuff. Have a great time. Don’t forget to er, study. ;)