Ryokans are a nice experience but I think 2 weeks at a Ryokan is a waste of money. A night or two would probably do.
The whole country is WTF, so there are too many things to mention. But a couple things are:
-inflexible adherence to rules and procedures. Ask for extra cheese or no ketchup and the cashier's jaw will hit the floor.
-related to that nobody will undermine authority so if you hit a brick wall ask for the manager right away.
-people are indirect and often communicate through subtleties they expect you to pick up on. If a restaurant is full or closing pretty soon they might not turn you away, but they might say seating you will be "a little difficult", and things like that.
-people want to be thought of as helpful at all costs even if it means being dishonest, so when you ask for directions for example, even if they don't know the right way, they will point you in some random direction. You have to watch them to judge how certain they seem about it.
-the level of English here is pathetic for a developed country. They don't understand sentences, but they do understand a lot of English words because they're used in advertisements and stuff. So "Do you know if there's a drugstore around here?" won't be understood but "Excuse me -- MEDICINE SHOP?" probably will be.
Hope that helps a bit. As a foreigner there are no unforgiveable faux pas, because they don't expect you to really understand their ways.