Hello there DancingToTheEternity 
 
I have been studying Japanese culture for about 4-5 years now..I've done plenty of reading online and as well in books..I have one book, that came out 7 year ago, in particular that has been such a great insight to Japanese culture and I always go back onto it if I need any information...I'll type out some things in this great book.
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Customs and etiquette
However Westernized modern Japan may appear, traditional etiquette continues to be very important. Most Japanese expect that, as a visitor, you will not understand the complexities of their social behavior, and that you will behave according to your Western rules. However, evidence of a basic understanding of a Japanese values and a respect for them will certainly be appreciated, enjoyed, and acknowledged by the people you meet.
Bowing
The Japanese bow a lot to each other on meeting or departing. The depth and frequency of the bows depends on the status of the people involved. To be on the safe side, imitate any bows you receive. Hold both arms straight and bow with the upper body. Shaking hands is an alternative way of introducing yourself and is still a novelty to the Japanese. However a strong shake is not needed and would not be understand.
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The majority of the restaurants will have a knife and fork to eat,  as well as take credit cards, this is more true for more of the modern restaurants of course..So be sure
I really recommend getting any books you can on Japan and visiting reliable tourist sites who let you know about these kind of things..Good luck 

 , If you need to know anything else feel free to ask