Firstly you need to recognise that many Japanese restaurants are specialist shops so try and figure out what kind of restaurant you are in. It's very unhelpful to ask for the vegetarian menu in a BBQ restaurant or steak house! Red lanterns outside a shop mean that they are a drinking establishment and also serve alcohol.
When you walk into a restaurant unless there is a queue of waiting people the staff will first of all ask you how many people are in your party. Show how many people with your fingers, this is
how Japanese people do it, so don't feel embarrassed.
If it is a large establishment you will then be asked 'smoking or non-smoking' (thats right you can still smoke in bars and restaurants in Japan!) if its a small place you can probably smoke anywhere.
You will then be shown to your table.
The menu will probably be in Japanese, but there may be wax models of the food on display outside. These can be very useful. Some busy places use a ticket machine where you buy a ticket with your choice printed on it from a vending machine, you then pass this to the staff who will prepare your order. These can be tricky to use if you can't read, so ask the staff for help.
If the menu is all in Japanese, instead of pointing wildly and at random, you can ask the staff for their recomendation by asking "o su su me wa?" or you can say "ma ka se shi mas" which means "I'll let you decide for me." Chances are that you will get something delicious and reasonably priced.
Many restaurants have a button on the table to call the waiting staff if you need them, if there is no button try calling "su mi ma sen!" literally "excuse me!"
In some restaurants after the staff bring your order they will put the paper that they took the order on face down on the table. When you leave, take this paper to the till where they will
calculate the bill.
When you pay you will be asked if you are paying all together or individually, either is accptable.
"Ba ra ba ra" is seperately.
"Issho" is together.
Don't try to leave a tip.