The underlying idea: do not disturb others
Before memorising loose rules, it helps to understand the thread that links them. In Japan almost all etiquette revolves around one concept: meiwaku, the nuisance or hindrance we cause to those around us. The idea is simple: in a country where many people live and move in very compact spaces — packed trains, narrow streets, small restaurants — coexistence works because everyone tries not to inconvenience others.
From this come the traits that stand out most on arrival: the silence on transport, the order of the queues, the cleanliness of the streets even though there are hardly any bins. They are not imposed rules, but a tacit agreement learned from childhood that sustains collective harmony, the wa. If you understand this, almost everything else follows on its own: when in doubt, ask yourself whether what you are about to do might bother someone.
From that same root come two other traits you will notice straight away. One is punctuality: trains leave at the exact minute and appointments are kept to the letter, so it is worth arriving on time (or a little early) for a reservation or a tour. The other is omotenashi, the attentive, anticipatory hospitality with which a guest or customer is treated; that care for others is the kind face of the same principle of not disturbing, and it is exactly what is appreciated to return with a gesture of respect.