I just ran across your post. I'm happy to help out. What part of Japan will you be visiting? I lived there for nine years so I have some experience with this.
Below are some comments I wrote for a friend who recently visited there followed by some links we put together for him.
I'll check with my wife later for a way to say you are allergic to shellfish. My guess is that there is not a catch-all term like we have in English. You may have to list several things like shrimp, oysters, clams, ...
I have no idea about skype. I don't use it now and it didn't exist when was in Japan. You can make an international call from most any public phone. The grey phones are OK. There should be some instructions about any prefix you need to dial international. The US country code is 1.
I say grey phone because Japan has color coded public phones. This is mostly of historical interest. However, there are probably still a number of pink phones in restaurants or hotel lobbies. These cannot be used for overseas calls.
I left Japan in 2003. At the time public phones were rapidly disappearing since everyone has a cell phone.
To order a beer it depends on where you are. At most restaurants they only serve one brand of beer so you just need to say "biiru onegaishimasu" and maybe hold up two fingers. In a shop you could say "sapporo futatsu onegaishimasu". If you are in a drinking place and want to sound like a pro you could try "Oneisan, daijoki nishoku onegaishimasu." That is a way to ask the young lady to bring you two giant draft beers. These are often 750cc to 1000cc.http://blog.e-otegami.net/beer123/image/daijokki.jpg
It is a little complicated because in Japanese counting is very complicated. Almost every number is associated with a counting word. Kind of like in English we don't just say "give me two socks", we say "give me two pair of socks." There is no way you can learn this in a short time.
However, as you are a foreigner most people will cut you some slack and you can muddle through with holding up two or three fingers when asking for something. If you are trying to learn words then you can use hitotsu, futatsu, mitsu, etc. To form the numbers six through nine open one hand and press the appropriate number of fingers into your open palm with the other had. For example, to indicate seven open one hand and press two fingers into your palm.
To indicate you don't have something or some other similar negative meaning cross you arms in an X pattern. In general, X means no (absent, broken, wrong) and O means yes (present, OK, working, good).
The most important word to learn is "domo." It means nothing and everything. It is like social lubrication. When you might say thank you or please or excuse me or many other situations you can just say domo. Maybe you can first say arigatou then as the conversation goes on you can start repeating "domo."
Another one is "sugoi." It is used a lot to express astonishment. Kind of like we use "wow", "really!", "amazing", etc. You'll hear it a lot.
Another is "ne" (nay). Often the end of a sentence is punctuated with this. It just adds emphasis. Kind of like "you know" in English.
If you'll be traveling anywhere outside Tokyo you'll probably want to get a Japan Rail Pass. It costs a few hundred dollars for a two week pass. That is about the price of one round trip to Osaka. Then the rest of your travel is free.http://www.kintetsu.com/jrpass/?gcli...FREDWAodpT783A
In Tokyo Asakusa is interesting. It has a large shrine and a long walkway up to the shrine filled with little outdoor vendors. It very close to Akihabara, the electronics district. These are also not too far from the Emperor's Palace and Ginza. Ginza is the district with the huge department stores.
From Tokyo you could take a one day bus tour to Mt. Fuji.
From Tokyo you could take a one day train tour to Nikko. Probably an overnight stay would be less hectic. This set of shrines honors the last shogun. It is ornate and colorful. The scenery is nice as it is set in the mountains.
Ueno Park has lots of museums. The Tokyo National Museum is a huge structure with lots of cultural Japanese items.http://www.planetware.com/tokyo/ueno...jpn-kn-tnm.htm
Shibuya is on the west side of Tokyo. It is where the young kids hang out. It is an interesting area to walk through just to people watch and window shop. Harajuku is nearby. Another nice place to people watch and window shop.
You might want to take in a Kabuki show. These go on for hours but you can get a ticket for a shorter duration (30 minutes or an hour). These are stage plays with colorful costumes and sets and live music. There is a famous theater near Ginza.
Also, through a travel agent you can probably find a Geisha show or similar cultural presentation. They have them in both Kyoto and Tokyo. Kyoto would be better.
Sanju-Sangen-do is an interesting temple. Inside are something like a thousand statues of Buddha culminating in one large statue in the center. They used to have archery tournaments here indoors. Because the roof is really low it took a powerful archer to shoot an arrow the length of the building and hit the target without hitting the ceiling.
Kiyomizu-Dera is interesting. It is a large temple built very high on a lattice of logs. Lots of shops on the road leading to the entrance. Everyone who goes to Kyoto visits here.
Kinkaku-ji is a very nice looking building surrounded by a pond. The interesting thing is that the whole building is covered in gold leaf. Pretty amazing.
Ryo-an-ji: very near Kinkaku-ji. Famous for the rock garden. There are a dozen or so large rocks set in a garden where the ground is covered with small gravel. Every day the monks rake the gravel so it has many straight lines left from the raking.
Heian-jingu: Large place with stunning red highlights.
Daibutsu: Huge wooden building with giant statue of the Buddha.
Imperial Palace: http://www.japan-guide.com/e/e3017.html
Nikko: (one to two hours from Tokyo)
Tosyo-gu Shrine: http://www.nikko-jp.org/english/index.htmlhttp://wikitravel.org/en/Nikko
Kinkaku-ji Temple: http://www.japan-guide.com/e/e3908.html
Heian-jingu Shurine: http://www.heianjingu.or.jp/index_e.html
Nara, Daibutsu (Biggest Buddhist Statue in the world)http://narashikanko.jp/english/menu/menu_2.htmlhttp://www.narakotsu.co.jp/teikan/te...an/tour_1.html