Credit goes to me and some other members of gamefaqs most of all ReignOfDestiny.

Yato: 1st Opponent during Independent Tournament. Also, Amihama Invaders.
Asahi Noir-draft: Kirizame -Amihama eight.
Ayade: Kanzaki during "A Deceptive Price" event.(needs Aleshaft to master. Jubei has this. Amihama eight, Normal or higher.)
Sadaha: Reddo Akagi
Hoodlum: Generic NPC
Hassu: Generic NPC. Possible higher chance from Mission related enemies
Impenetra: Generic NPC

Goshi: Jubei- Amihama eight
Jackson: Kotetsu- Amihama eight
Mushin: Starting style
Zabi: Gambling den Mistress, Amihama eight. Wait for everyone to clear out.
Gan: Sensei (needs New World to master. Sensei has this on Normal or higher difficulty.)
Shamei: Mayu.
Kudoi: Kotobuki (Chu-dan/Jo-dan)
Invinciba: Generic NPC

Tsubo: Kobato Amihama eight.
Osha: Generic NPC. Higher chance possible from Mission related enemies.
Nightly Delights: Generic NPC
Bokunen: Suzume- Amihama eight
Tenshin: Gunji Dojima (needs Black Mark't, Bamboozler or Shady Deal to master. Dojima can have any of these. Shady deal on Normal or higher.)
Kuki: 1st opponent during Prajna Path Tournament. Amihama 8 Invaders
Sekoi: Generic NPCs
Cantgetmi: Generic NPCs

Flannel: Shingeru Moro -Road to Ruin ending.
Tokyu: Given when you take over the dojo. (Can only earn skill points to master from Doho Challengers...or just use Scrolls)
Bugyo: Commander, Amihama eight. (Needs Haruyuki to master. Shigeru Moro has this
most commonly on Normal. - Road to Ruin ending)
Windsor: Melinda Megamelon
Kinugawa: Kinugawa (Waki/Chu-dan/One-Handed) - True Ending
Isobe: Generic NPCs
Hanima: Generic NPCs
Noble: Generic NPCs Higher Chance from Mission related Enemies
Common: Blondie Knights at the consulate.

Sa-Muraitto: Blind Samurai Tournament oppenent. (needs Lost Prayer to master. Sensei has this on normal difficulty.)
Hanza: Gambling den Book Keeper. Amihama 8
Jochaku: Generic NPCs and Mission Targets
Kasshin: Kogure.
Sexua: Generic NPCs and Mission Targets
Kinen: NPCs
Victorious: Consulate event "funding the hospital".
Perfect: NPCs

Torikata: NPCs
Wisdom: New Commander, kill Melinda. New Commander should pop up.
Senba: Hosakawa, Tournament Magistrate path
Ulster: J.J.
Kyoji: Invader Amihama eight. Or Kinugawa's double, during Fevered Spirits ending.
(Needs Tailbwnd to master. Invaders can have this on any difficulty. The fake
Kinugawa will also carry this.)
South Range: Clean Samurai. Homeless jobs
Goyo: Random Theif-taker Or "Plea Bargain."

Saiga: Generic NPCs. Suggest farming Black Masks. 5 Star Dojo Challenger Bikini Sister- Shinobi
Urahara: Madara.
Genba: Murderer in "The Players". Bikini Sister
Asuka: Orochi, Amihama eight.
Toho: 5star dojo challenger. Blue Kimono, straw mask. (Needs Morning Moon to master. Orochi can carry this on normal or higher. Amihama eight.)
Oniwa: Generic NPCs. Bikini Sister
Fumo: Generic NPCs- Farm Yakuza mission "Amihama's Womanizer". Bikini Sister
Climactic: Same as Above.

Harmonious: Demonscale Commander (Replaces Melinda in Prajna Path Tournament if she was killed ) Or Manmaru- Amihama eight.
Haten: Manmaru -Amihama eight.
Kantetsu: Tournament opponent. Prajna path. Kill megamelons before the tourney. Also Possible from Dual-Arms Dojo
Gokon: Chika
Dual Manifest: Demonscale Gate Keeper Prajnas path if Dual- Shinobi unlocked in menu before Dual Arms.

Junky: Ekubo, yakuza mission "Empress needs no competition" Or 5 star dojo challenger- The Dual Shinobi Bikini Sister
Kogara: Same as Above.
Mosu: Same as above.
Hara: Toguro if Dual- Arms unlocked in menu before Dual-Shinobi.

Blossom: Hyouka- Amihama eight.
Aido: Yuri
Fukuo: Generic NPCs
Masuo: Spear wielding tounament opponent. Foreigner path.
Scripturist: Generic NPCs.
Kongo: Spear wielding tounament opponent. Foreigner path.
Daido: Generic NPCs
Gekisho: Starting style.

Adamantine: Casino guards. Or the Body Guard on the Black Ship.
Gachinko: Tournament martial artist Name coming. Foreigner path.
Shoji: Old Smithy, pre-Dojima taking over. (Needs Tiger Claw to master. The second
tournament opponent [foreigner path] has this on hard.)
Casual: Starting Stlye
Yubari: Shigeru Moro - except Road to Ruin Ending.
Nightly Pleasure: Dojo challenger, five star, must have all female students.
Asasho: Thief mission with the sumo wrestlers. Old Man in the Homeless
mission "Grandpa's Memories" . Human Pigs the "Rescuing J.J." Event.
(Needs Dragon Claw to master. Gachinko Tournament opponent has these on Harakiri)