As you might have seen before, it is Japanese tradition to greet with a bow. Different types of bows have different meanings; a longer bow with a deep waist bend shows respect in formal situations, whereas a small head nod is used in more informal settings. Bowing is used to show gratitude and thanks, apologize, and make polite requests. Japanese understand that foreigners are not familiar with their bowing customs, and they do not mind if you just give a small nod. Usually people do not put their hands together when they bow in the country. If a greeting takes place on the tatami floor (which can happen often in Japan), people will bow on their knees.
If you enter a temple, note that you might need to take off your shoes. If this is the case, leave them at the entrance or put them in the bag that is given to you. Remember to wear nice socks for these situations. Usually, you are allowed to take pictures at temples, but watch out for signs indicating if photography is forbidden.
Unlike in other parts of the world, Japan has very few trash cans. It is common for locals to carry around a bag and hold their own trash until they can properly dispose of it; you will probably need to do this as well. Recycling is common, and locals like to conserve and reuse out of pride for their country and respect for their environment. It is considered rude to talk loudly in public, even when you are outside. Be aware of your tone of voice when in public settings, and keep it at a softer level than you are usually accustomed to.