However, it honestly offends me when you say I should just put my values "on hold". It might not be convenient for others, but I'm not going to put my moral values on the side for convenience, actually the way humans treat animals is the selfish act, not me going to Japan intending to eat in a cruelty free manner.
First off let me say that Rabbityama put it very well. However I did want to make some additions that address the issues you raise.
Please don't be offended by the suggestion to put your values on hold. Obviously we understand that many people simply can't give up being vegetarian/vegan for moral or religious reasons, and if that is you than this clearly wouldn't be an option. No need to explain your moralization, just feel free to ignore that part of the advice.
As you know, being vegan is a lot of work, and being vegan in Japan is even more so. But you do have options. From my experiences working and travelling with vegans/vegetarians in Japan, there seems to be three approaches that people commonly take, each with its pros and cons.
The first is to take a sort "what I don't know won't hurt me" attitude when eating food. Do your best to avoid animal products, but understand that you will probably eat some unintentionally.
The second is to stringently read labels and only eat things that you can verify were not made with animal products. More than likely you will have an extremely limited set of things you can eat, especially if you don't read Japanese. I travelled with one vegan guy once who employed this method, and he basically ate kappamaki and edamame the entire trip. And he could read Japanese, which leads me to believe that you should just avoid most prepackaged foods and restaurants altogether.
The third is a little more involved, where you would buy/bring all your own food with you and cook your meals yourself. I hear halal tourists often take this route since halal restaurants are rare/impossible to find in Japan. Obviously, that's a lot of work for a short stay, and may not be possible at some accommodations.
Anyway, good luck with your studies. For a start you can look up some of the words like dairy, fish, etc. in the dictionary so you can study them and be prepared:http://www.csse.monash.edu.au/~jwb/cgi-bin/wwwjdic.cgi?1C