I have been doing a little research regarding etiquette, etc. Partly because it pertains to my curriculum project (part of growing up in a particular region is following (or not) the customs, etc.) but mostly because I don't want to look like an ignorant American when we get there.
So, in my search I found this website. It has some great information. If you go toward the bottom of the page you can click on Etiquette and find instructions on using Japanese toilets, entering shrines, etc. If not useful, some of it is most definately intersting (and humorous). But beware, if you want to watch the video demonstration on how to use the (pit) toilet you'll have to do so at home for the LAUSD sensor does not permit that content. Consequently I have yet to see the video. Poo. But I think I can gather what to do if need be.
Happy browsing!
http://www.japan-guide.com/