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If you decide to go outside the major cities, prepare to be looked at oddly, and with serious contempt, especially in the rural areas*hell, that may even happen within the major cities, at some points*. Watch your bum on crowded trains, 'cause there may be a guy(or girl, possibly) there waiting to get a peek at it, or a handful. Remember: Homogeneous society =/= foreigner friendly.

I don't really know too much about social norms and such over there, so all I can do is speak from personal experience. Both of the times I was over there I didn't have any problems with strangers trying anything with me (I also stayed away from "seedy" areas, never really understood the appeal of them, but to each their own). The most physical contact I had with a stranger was a little kid petting my hair on the bus (I have very long blond hair). If you are really concerned, stay away from the trains during rush hour, or if you must, they do have cars on trains that are designated for women only. I've visited all areas from extremely urban to extremely rural. Yeah you get more looks when you are in rural areas, but you gotta realize, all they really know are asain attributes, so of course when they see something different they are gonna look at it. It's in human nature. Take Zoos for example. We build complexes specifically designed for gawking at what we don't normally get to see lol. If you have blue hair, your probably pretty used to getting looks lol; our society has a tendency to do that too lol. Every now and then you run into someone who will have a bit of an attitude with you or something. One of the times I was there I worked on a Naval Base, so from time to time I would run into someone who had distaste for me (probably because they've run into one too many bad examples of Americans, seeing as a lot of the sailors were very good at portraying a bad image, especially when drunk). But Take it all with a grain of salt. Try not to be weighed down by expectations/worries, and just focus on having a good time.

Honestly? You won't have too much to worry about. I went there two summers ago and the most that happened to me was a random guy asking me to take a purikura with him... and the group of students wanting to hang out. You will get stares, but don't let that concern you. Also, even if you were to go on a crowded subway there is no way (at least from my experience) that a guy or girl will even TRY to feel you up simply because you ARE a foreigner and in their eyes we tend to do unexpected things when touched. Like scream at, kick, slap or punch the offending person. blaugh
Do so enjoy yourself, it's a fun place to be. Though I want to say to remember to finish all the rice you are given (every last grain) if you go out and do not put any "common" sauces on it, like sugar or soy, since this is considered an insult.

Haha, I always finish my white rice without sauces. I mean. GEEZE I love white rice that much! ^^

My family is very old-fashioned and we follow a lot of old etiquette from Japan.. As someone mentioned, never put anything on white rice unless you've ordered something that already has under it (donburi, curry-rice), in fact, I was told by my aunt that if you're eating in a nice / traditional setting, rice should not be eaten until the very end. When eating nigiri, don't dip the entire thing into shoyu either, you should take off the fish from the top and dip it in the shoyu, usually they will provide you with a dab of wasabi underneath.

If you speak Japanese well, that's good, but if you're still learning, you may want to ask if the person helping you speaks English, especially in vendor/small business settings. When I was in Osaka, I was talking to a street vendor and his Japanese kept deviating from Hyojungo (which is what I'm used to speaking with my family) and it starts to get confusing. But using English is very helpful (though many older people don't use it).

You should be careful depending on where you are, apparently places like Shinjuku can be dangerous at night, but I didn't notice any of that while I was there.

If you want to buy clothes, I can guarantee that you'll most likely pay more than you normally would...A lot of Japanese fashions are imported from Europe, so it gets really expensive to buy - even if you're buying things made in Japan too.
Also, if you're really tall, you may not have a size that will fit you, because Japanese sizes don't always accommodate Western physical build.

That's about all I can think of at the moment/need to go do some homework.

TTyl!