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Thunder Rift Regionsby Giorgio
From what I have learned so far there are humans present all over the valley, and no strong central authority. Kleine is isolated far to the north and the Black Knight is way to the south, so I would write them up independently.
Melinir and Torlynn are not only close geographically, they are in the same section of the core TR module, they are linked by roads and can be considered part of the same "human community", thus I would describe them together. I would also add Edgewater and Mage Island for the same reasons.
Now the areas your mention, I am still waiting on your response in the Races of Thunder Rift post, but taking some info from the Thunder Rift Regions post, rereading the TR core module, and adding a few extras I would redo it as:
Civilized Regions II
Farolas Hills: Dwarven Lands (Hearth-home, Stonefast) Kleine Region: Human Lands (Kleine) Lands of the Black Knight: Human Lands (Black Knight Keep) Melinir Hills: Human lands (Edgewater, Mage Island, Melinir, Torlynn) Gauntlin Forest, Western: Elven Lands (Silvercrest) The Wailing Plateau: Rakasta Lands (Aratasharai)
Wild Regions II
Black Swamp: Carnivorous Trees, Lizardmen, Newts, Trolls Brichtwood: Centaurs, Harpies, Trents Bone Hills: Dragon, Goblins, Orcs, Wyverns Burning Hills: Dire Wolves, Gnomes, Goblins, Hobgoblins, Kobolds, Wyverns Farolas Hills: Orcs Grasslands, Central: Centaurs, Gnolls, Harpies, Humans, Owlbears Grasslands, Northern: Bugbears, Centaurs, Gnolls, Goblins, Humans, Kobolds, Orcs Grasslands, Southern: Centaurs, Gnolls, Harpies, Humans, Owlbears Gauntlin Forest, Eastern: Gnolls, Giant Spiders Gauntlin Forest, Northern: Bugbears, Gnolls Gloomfens: Undead Grakken Wood: Ogres, Owlbears Horned Hills: Goblins, Hobgoblins, Minotaurs, Wyverns Kraal: Newts Marshwood: Lizardmen, Undead Melinir Hills: Brigands, Dire Wolves, Goblins, Kobolds, Rakasta, Ratlings Wizardspire: Undead
-Halflings donít have a home of their own, but they can be found in the Melinir Hills alongside the humans.
-Kobolds: I expect them to be hunted to extinction by orcs and hobgoblins, thus I removed them from places where these races are present (except for a minor presence in the Northern Grasslands)
-Wyverns: in addition to being found in the hills surrounding the valley, a nest is believed to be located somewhere within the Gauntlin Forest.
For even more monsters to choose from, take a look at PF Monsters by Terrain.
animated object, barghest, basilisk, clay golem, deathweb[AP], devourer, dlurgraven [3PP], dog, doppelganger, fire beetle, flesh golem, gargoyle, ghost, ghoul, giant ant, giant spider, greater barghest, greater shadow, hell hound, homunculus, hound of tindalos[AP], iron cobra, iron golem, kyton, lich, mimic, minotaur, mohrg, moonflower [AP], mummy, nessian warhound, night monarch[AP], rakshasa, rat swarm, redcap[AP], riding dog, shadow, shining child of thassilon[AP], skeletal champion, skeleton, skull ripper [AP], spectre, spider swarm, stone golem, tarrasque, totenmaske [AP], vampire, vargouille, werewolf, wight, wood golem, wraith, xill, yeth hound, yethazmari[AP], zombie
Any Terrain (Temperate)
cyclops, bat swarm, dire bat, lizard, rat, venomous snake
Forest (Temperate); Grakken Wood, The Gauntlin Forest
assassin vine, bat, boar, centaur, dire boar, dire tiger, dire wolf, dryad, ercinee[AP], ettercap, giant mantis, giant scorpion, giant stag beetle, giant wasp, goblin, goblin dog, greater tengu, yamabushi [3PP], green dragon, half-celestial unicorn, hawk, kobold, nymph, owl, owlbear, pixie, pseudodragon, satyr, shambling mound, tiger, toad, treant, unicorn, wasp swarm, witchfire[AP], wolf, worg, yellow musk creeper
Rivers/Lakes; Drake River, Lake Ganif
aboleth, constrictor snake, crocodile, dire crocodile, electric eel
Hills (Temperate); Burning Hills, Bone Hills, Farolas Hills, Horned Hills
bulette, chimera, gorgon, griffon, hill giant, hobgoblin, ogre, orc, weasel, wyvern
argorth[AP],bugbear, cloud giant, eagle, giant eagle, greater tengu, yamabushi [3PP], orc, silver dragon, tengu
Plains (Temperate); The Great Grasslands
ankheg, aurochs, bison, cat, centaur, cockatrice, dire tiger, giant scorpion, goblin, gorgon, guardian naga, horse, pegasus, pony, worg
Swamp (Temperate); Marshland, Black Swamp
boggard, brineborn marsh giant[AP], chuul, dire tiger, dracolisk, froghemoth, giant flytrap, giant frog, giant leech, giant slug, goblin dog, green hag, harpy, hydra, leech swarm, lizardfolk, marsh giant[AP], medusa, ochre jelly, shambling mound, spirit naga, stirge, will-o'-wisp, witchfire[AP]
Urban; Human lands
aasimar, dire rat, tengu, tiefling, wererat
To above I would add Mystara specific monsters, but I don't have that info on hand, so I will leave that up to more experienced monster lore scholars!