The Role of Honor: How it's used, how it's gained, how I should treat it.
It's a measure of doing what is right. If you're losing it, you're being a villain. If you're gaining it, a righteous samurai.
As a player, you don't use it, per se. As a GM, you inform players of whether they are living up to samurai morals with it.
The Role of Courtiers: Both inside and outside of combat (especially outside).
In combat: survive. That's it. Some may also be combat capable, but it's neither their giri (duty) nor their role. A few (Magistrates) might be combatants, but they are the exception.
Outside of combat: some are the face-men (talkers, con artists, negotiators, diplomats), some are artisans (which is good for duels of art), and some are information gatherers (magistrates, spies)
The Role of Clans: I can tell there is a lot of emphasis here, but I don't really understand its purpose.
You are part of larger groups. The family (more properly, sept, a division of a clan) is a sub-clan. You have multiple duties as a samurai: To the Emperor (The Daimyō of all), To your Clan's Daimyō, your Family's Daimyō, Your local Daimyō, your wife, your parents & siblings, your family members, and your clan mates. What ranking you put those into defines, in many ways, how to play the character.
Mechanically, Clan determines what schools are available to you, and what families.
Socially, Outside your clan, you're pretty much interchangeable with any other non-daimyo non-magistrate of your clan. Only within is your personal identity valued. And likewise, unless duty demands it, you should avoid members of other clans; they are not allies, per se... except when it comes to fighting Oni. Some GM's ignore this aspect, tho'.
The Clans can, in many ways, be thought of as nations within the Union of Rokugan. They often have fought wars with each other.
The Role of Artisans and Geisha: Are these "classes"? how do they fit in the game?
Artisans are there to win duels of Art. See Way of the Courtesan for more details on that.
Geisha are non-people. They are there to entertain samurai and to be spies, and as romantic plot objects. They are not, generally, suitable as PC's. (Historically, they bordered on indentured slaves.)
The Different Archetypes which are germane to the setting
The big archetypes of the Samurai Genre...
The Bushi's Bushi: the combat monster. Big, strong, tough, often not too bright. Honorable, but manipulated. If you phrase something as dishonorable, he won't do it; if you convince him Honor demands it, you won't stop him without killing him. High earth ring, high willpower.
The Thinking Bushi: A less combat-capable bushi, but still quite lethal, he tends to avoid combats, but can hold his own. Experienced bushi of this type are often excellent captains and generals.
The sneaky bushi: not a skulker and hider, but a political creature. gets others to do his handiwork. Often a courtier, but not always.
The Yojimbo: the devoted bodyguard. Once assigned a charge, nothing, not even his own dishonor, will cause him to willingly let harm befall his charge. Often, this also involves thwarting the will of the charge...
The Wise Warrior Monk: dispenser of advice and, when needed, but-kicking. Often possessed of quite the temper, but it's long, slow, and when riled, unstoppable. Usually a retired samurai.
The Silly Monk: usually a young monk, who does stupid things, but learns from the experiences. Often comic relief, and often shares bits of wisdom without realizing it.
The quiet master of the Monastery: ancient, withered, and wise beyond reason. Not usually suitable for PC's. Basically, a living encyclopedia, but also one which, being retired samurai, is capable of delivery of rather surprising violence when absolutely needed.
The Magistrate: Tasked to keep the peace, and to investigate crimes. Half courtier, half warrior, and half spy... Subtypes include the Honest Magistrate (often played the fool), the detective (who has to then coerce confessions and witnesses), and the slayer (who figures out the guilty, then kills them while they "resist arrest").
The Geisha: usually a love interest. Always duplicitous in some way. And one who falls in love with her is doomed. Not samurai.
The Rōnin: Masterless, and honorless, he's either to be pitied, abused, or paid to be sacrificed in battle. The best are incredible, but often treachery or cowardice is how a Rōnin makes it to old age.
The Shinobu: the spy, the assassin. Hides in plain sight, pretending to be one of the above, or a servant of one of the above. Usually killed when exposed.
Fantasy Samurai Archetypes
The Shugenja: Healer, priest and wizard. Makes children nervous, and worries bushi. Unless, of course, he's YOUR clan's Shugenja. Then he just creeps you out until he blasts the goo out of that there oni, or glues you back together after a battle.
The Chanbara Monk: The guy making the 20m leaps and throwing monsters. Physics went out the window when he entered the room. Naruto, were he not a ninja. In game, there have been a few schools that can support this.
Demon Hunters: usually in the game, these are magistrates or members of the Crab Clan. In the broader samurai literature, they are often monks or priests, often madmen.