Although I have noted which families are primarily bushi (martial), shugenja (arcane), and ninja (do they really exist?), this is more likely which school you (or your ancestors) would have trained due to their individual proclivities. If a warrior family (or its vassal) produces a child with the talent to speak to the spirits, she will be sure to train as a shugenja, and vice versa. This also gives more options for multiple motivations.
To layer your character’s background further, you can have multiple reasons (or a claimed reason and a secret one) for leaving your clan and/or joining the Crab. You could also respect your heritage from more than one clan by marriage. Any ideas you don’t use will be helpful for my NPCs, although the ninja and hengeyōkai likely wouldn’t show their true nature (possibly masquerading as other backgrounds), so you won’t necessarily know which ones they are.
Any Samurai: Your liege died with no heir, so you find yourself thrown to the waves.
Any Samurai: Your liege was disgraced and removed, so you must find your own honor.
Any Samurai: You disagreed with your liege’s policies and chose to show your opposition through desertion rather than suicide.
Any Samurai: You could not accept the legal settlement of the blood feud by a Crane’s revenge against your kin, so you left your clan to avenge the insult in another way.
Any Samurai: You had a second chance at life when you returned to Rokugan from the realm of the dead via Oblivion’s Gate. With your previous lieges dead, you seek fealty to the Crab.
Any Samurai except Crab: Your family agreed with your wish to fight the true evils of the Shadowlands and allowed you to go to a place where you could, possibly finding the fate of a kinsman who never returned while you’re at it.
Any Samurai except Crab: Although you have left your family in name, you are really just here to keep an eye on the Crab.
Any Samurai except Crab/Unicorn: You were too wild to serve as a vassal in one of the “civilized” clans, so you hope to find a place among the Crab berserkers.
Those born to the Crab give an alternative to just joining the clan.
Crab: Whatever failure you or your ancestors perpetrated, you hope to redeem yourself by earning fealty once more to your old lieges.
Crab (Hida Bushi): Although you are born to privilege, you are a Crab, not some milksop Crane, so you may as well along on the mission to assess (and to show your worth to) your future subordinates.
The Crane are the other clan most connected to the plot, as they are at war with the Crab. This makes for a character who is connected to the plot, but is conflicted in the war.
Crane (Asahina Shugenja): Taken as a hostage by the Crab during an early battle of the Second Yasuki War, you have come to see the honesty of their ways, fighting true evil even as the immoral political conflict wears on. You hope that by the time you have grown out what hair is bleached white, you will be accepted as a vassal of the rightful Yasuki.
The Dragon are one of the northern clans, but there are still some hooks (including one for Hoshi rōnin below).
Dragon (Mirumoto Bushi): Coming to the south as a guard for the Dragon ambassador to the Crab, you choose to show your loyalty to your hosts.
The Mantis were until recently a Minor Clan of mercenaries, so they fit in everywhere.
Mantis (Tsuruchi/Yoritomo Bushi): Shamed by the view of your clan as bounty hunters and mercenaries using peasant weapons, you hope to legitimize your service to your longtime employers by becoming a vassal.
The Phoenix as a whole are distant, but they do have those who move through the Empire.
Phoenix (Asako Bushi): Your family’s inquisitors have long worked with the Kuni Witch Hunters and other clans to root out evil magic, and where your loyalty to your own clan alone has been questioned, you seek to strengthen your ties with your allies and take the fight to the Shadowlands.
The Scorpion have men everywhere. They share the Crab’s concept of philosophy over honor, but take it in the opposite direction, becoming great deceivers in court.
Scorpion (Shosuro Ninja): One secret you have found is that some will kill to keep secrets. To preserve your life, you sought to leave your clan and find your fortune elsewhere.
The Unicorn are the Crab’s closest allies (unsurprising considering their views on politics and society versus action), although that means that they need not necessarily join that clan to serve their causes.
Unicorn (Horiuchi/Iuchi Shugenja): Your studies in the foreign name magic talismans would be furthered by comparison with similar abilities of ratling conjurers of the Shadowlands. Cut off from the power of the Spirit Realms, your family will master any traditions it can.
Unicorn (Moto Bushi): Although your family’s quest against their Tainted brothers was ended with the Dark Moto’s destruction before Oblivion’s Gate, you cannot give up the purpose that defined your ancestors for 300 years. You will join the Crab to continue the fight against the Shadowlands until no samurai ever falls to its Taint again.
Unicorn (Otaku/Shinjō Bushi): After the Shinjo lost their position as ruling family of the Unicorn, you saw Hida (ne Shinjō) Yasamura as your true liege, so you seek to follow his widow O-Ushi and sons Kuroda and Kuon, leaving your old clan with the blessing of your family. Or did your departure have something to do with the purge of Kolat influence among the horse-lords?
And some of these other factions may come into play as well. The pragmatic Crab are (as the Twenty Goblin Winter exemplifies) more accepting of ronin, commoners, and outsiders, as long as they are useful.
Imperial Families (Otomo Bushi): After the Clan War, Akodo Totsuri was raised by public acclaim to be the founder of the new imperial dynasty, even though your family is directly descended from Hantei I. Sick of these politics, you left to fight the Shadowlands, and possibly to aid the Yasuki against the Crane usurpers in the meantime.
Fox (Kitsune Shugenja): Because of your odd practice of taboos, you believe the Crab would be more welcoming than less diverse clans.
Monkey (Fuzake Shugenja): Trained by Fuzake (formerly Yasuki) Garo, you were perturbed by the usurpation of the Yasuki name by another clan and chose to help. Your work serving the Empire as a whole will help you to adjust to another clan.
Sparrow (Suzume Bushi): With your family’s tradition of oral history, you choose to fight against your extravagant kin your ancestors left during the First Yasuki War.
Rōnin (Hoshi Bushi): When Hitomi banished your namesake from the Dragon, your family was taken in by fellow monks of the Brotherhood of Shinsei. You have heard of the disdain for the Togashi as being bound by blood tattoos rather than noble descent, so you hope to join a proper bushi family.
Rōnin (Scales of the Carp): All the smuggling you did with the Crane was to benefit the Crab financially. Now that the two are at open war, you seek to prove your loyalty to the defenders of the Empire.
Rōnin (Unbroken): Already touched by Taint, you have a place in the Shinomen Forest, but have spoken with the Kuni Witch Hunters of the Crab and know that if they will use the Lost, they will be willing to allow your fealty as you take the fight to the source as a true samurai.
Rōnin (Yotsu Bushi): Although Hantei XXXVIII gave your grandfather a family name and a jurisdiction in the Imperial City for defeating Bloodspeakers, the two great battles of the 12th century have left peace in the capital. You seek a place to join a true clan while still fighting blood magic, and the Twenty Goblin Winter is also a great place to find rōnin to send back to the Yotsu.
Commoner/Foreigner: Although you claim not to be tainted by the evil of the Bloodspeakers and Kolat, you agree that one can earn one’s station and fortune, and the most obvious way for advancement is the Twenty Goblin Winter.
Commoner/Foreigner: As you could never hope to win a political marriage with a samurai, you hope to be one of the few footmen to gain vassal status to court your love.
Commoner: No one but a samurai is as loyal to the Crab as you, so it is only proper that you prove your fealty by becoming a noble vassal yourself.
These are the ones that are not for humans:
Hengeyōkai: Your curiosity, sense of humor, or feeling of obligation to repay a favor has led you to infiltrate a group of human rōnin.
Kenku: The humans fighting evil could use a good teacher. Although you are not yet the most experienced, you are also keen to see how well the disciples of your swordmasters have been passing on their wisdom.
Ratling (Pristine Paw Tribe): Long days in the Shadowlands have withered the numbers of your people. Nameseeker Tik’ki’titev suggests that cementing alliances with the human warriors would be in your best interests. (The Pristine Paw (tentative name) is a tribe that I have created to fit my storyline. I feel ratlings are best represented by the razorclaw shifter player race.)