Calls within Japan are outrageously high and even using NTT's competitors saves little. However, local calls are cheap. Some Japanese collect cards with pictures of movie stars, etc. which are sold at a surcharge. Unless you are interested in this aspect of Japan, there are many pretty cards available without surcharge. Check how much you are paying against how much the card is imprinted for.
Transportation is very expensive.
Review railroad and subway monthly pass and multiple trip options. It is much cheaper to take a long vacation trip in Japan than several short ones as a long distance ticket gives you several days to complete your travel with intermediate stopovers. JR passes purchased overseas are not usable if your passport shows you are not a tourist. If you really want to drive a car in Japan, you need an international driver's permit, available in the US from AAA and good for 12 months, or a Japanese driver's license, a bureaucratic pain. If you want to register a car in Tokyo, you must prove you have a parking space.