Well, i thought of lots of cheap jokes about what not to do on your honeymoon, but thought better of it!
If you look in any good guidebook on Japan it will have some words to say on the doos and don'ts of Japanese etiquette.
The main ones I found were....
shoes. Make sure you take off your shoes at the appropriate times. Usually, if there is a raised wooden floor then you take off your shoes before stepping on the wooden floor. If in doubt, watch the locals. Also make sure you don't have holes in your socks
Nose blowing - very offensive to do this in public and you should sniff instead. TBH I found this one of the hardest to remember, because it is the opposite to my culture.
Don't point with your chopsticks or leave them sticking up in a bowl of rice.
As you are asking this question you are obviously a well mannered and considerate person so I don't think you will have any problems. You will undoubtedly get stares, but don't get uptight about it, I think a lot of it is to do with curiosity - especially with younger children who quite often point and stare

I never felt any of it was hostile.
The best way to get along is to learn some Japanese, if only the basic phrases - they get you a long way.
Hope you have a great time