This version works:
[CREATURE:SWAMP_MONSTER]
[DESCRIPTION:A tall and scaly creature that lives in swamps. It has no visible ears, a mouth full of sharp teeth, and two holes in its face instead of a nose.]
[NAME:swamp monster:swamp monsters:swamp monster]
[CASTE_NAME:swamp monster:swamp monsters:swamp monster]
[CREATURE_TILE:'S'][COLOR:3:0:0]
[INTELLIGENT]
[CANOPENDOORS]
[LIKES_FIGHTING]
[AMPHIBIOUS]
[BIOME:ANY_WETLAND]
[BIOME:ANY_TEMPERATE_FOREST]
[BIOME:SHRUBLAND_TEMPERATE]
[LARGE_ROAMING][DIFFICULTY:2][FREQUENCY:90] UBIQUITOUS
[POPULATION_NUMBER:10:20]
[CLUSTER_NUMBER:1:3]
[FREQUENCY:100]
[OUTSIDER_CONTROLLABLE]
[LOCAL_POPS_CONTROLLABLE]
[LOCAL_POPS_PRODUCE_HEROES]
BENIGN
[CLUSTER_NUMBER:1:3]
[LARGE_PREDATOR]
[PRONE_TO_RAGE:40]
[PREFSTRING:smooth scales]
[PREFSTRING:sharp claws]
[BODY:HUMANOID_NECK:2EYES:NOSE:2LUNGS:HEART:GUTS:ORGANS:HUMANOID_JOINTS:THROAT:NECK:SPINE:BRAIN:SKULL:5FINGERS:5TOES:MOUTH:TONGUE:FACIAL_FEATURES:TEETH:RIBCAGE]
[BODY_DETAIL_PLAN:STANDARD_MATERIALS]
[USE_MATERIAL_TEMPLATE:SCALE:SCALE_TEMPLATE]
[BODY_DETAIL_PLAN:STANDARD_TISSUES]
[USE_TISSUE_TEMPLATE:SCALE:SCALE_TEMPLATE]
[BODY_DETAIL_PLAN:VERTEBRATE_TISSUE_LAYERS:SCALE:FAT:MUSCLE:BONE:CARTILAGE]
[USE_MATERIAL_TEMPLATE:NAIL:NAIL_TEMPLATE]
[USE_TISSUE_TEMPLATE:NAIL:NAIL_TEMPLATE]
[TISSUE_LAYER:BY_CATEGORY:FINGER:NAIL:FRONT]
[TISSUE_LAYER:BY_CATEGORY:TOE:NAIL:FRONT]
[PLUS_TISSUE_LAYER:SCALE:BY_CATEGORY:THROAT]
[TL_MAJOR_ARTERIES]
[BODY_DETAIL_PLAN:STANDARD_HEAD_POSITIONS]
[BODY_DETAIL_PLAN:HUMANOID_HEAD_POSITIONS]
[BODY_DETAIL_PLAN:HUMANOID_RIBCAGE_POSITIONS]
[BODY_DETAIL_PLAN:HUMANOID_RELSIZES]
[USE_MATERIAL_TEMPLATE:SINEW:SINEW_TEMPLATE]
[TENDONS:LOCAL_CREATURE_MAT:SINEW:200]
[LIGAMENTS:LOCAL_CREATURE_MAT:SINEW:200]
[HAS_NERVES]
[USE_MATERIAL_TEMPLATE:BLOOD:BLOOD_TEMPLATE]
[BLOOD:LOCAL_CREATURE_MAT:BLOOD:LIQUID]
[CREATURE_CLASS:GENERAL_POISON]
[GETS_WOUND_INFECTIONS]
[GETS_INFECTIONS_FROM_ROT]
[BODY_SIZE:0:0:4200]
[BODY_SIZE:2:78:20500]
[BODY_SIZE:14:0:80000]
[NATURAL_SKILL:GRASP_STRIKE:8]
[BODY_APPEARANCE_MODIFIER:HEIGHT:70:75:90:97:105:110:125]
[APP_MOD_IMPORTANCE:500]
[BODY_APPEARANCE_MODIFIER:BROADNESS:70:75:90:97:105:110:125]
[APP_MOD_IMPORTANCE:500]
[SET_BP_GROUP:BY_CATEGORY:EYE]
[BP_APPEARANCE_MODIFIER:CLOSE_SET:0:70:90:100:110:130:200]
[APP_MOD_NOUN:eyes:PLURAL]
[BP_APPEARANCE_MODIFIER:DEEP_SET:0:70:90:100:110:130:200]
[APP_MOD_NOUN:eyes:PLURAL]
[BP_APPEARANCE_MODIFIER:ROUND_VS_NARROW:0:70:90:100:110:130:200]
[APP_MOD_NOUN:eyes:PLURAL]
[BP_APPEARANCE_MODIFIER:LARGE_IRIS:25:70:90:100:110:130:200]
[APP_MOD_NOUN:eyes:PLURAL]
[APP_MOD_DESC_RANGE:30:60:90:110:150:190]
[SET_BP_GROUP:BY_CATEGORY:LIP]
[BP_APPEARANCE_MODIFIER:THICKNESS:50:70:90:100:110:130:200]
[APP_MOD_NOUN:lips:PLURAL]
[APP_MOD_DESC_RANGE:55:70:90:110:150:190]
[SET_BP_GROUP:BY_CATEGORY:TOOTH]
[BP_APPEARANCE_MODIFIER:GAPS:0:70:90:100:110:130:200]
[APP_MOD_NOUN:teeth:PLURAL]
[BP_APPEARANCE_MODIFIER:LENGTH:100:100:100:100:100:100:100]
[APP_MOD_IMPORTANCE:1000]
[APP_MOD_NOUN:teeth:PLURAL]
[APP_MOD_DESC_RANGE:30:60:90:110:150:190]
[SET_BP_GROUP:BY_CATEGORY:SKULL]
[BP_APPEARANCE_MODIFIER:HIGH_CHEEKBONES:0:70:90:100:110:130:200]
[BP_APPEARANCE_MODIFIER:BROAD_CHIN:0:70:90:100:110:130:200]
[BP_APPEARANCE_MODIFIER:JUTTING_CHIN:0:70:90:100:110:130:200]
[BP_APPEARANCE_MODIFIER:SQUARE_CHIN:0:70:90:100:110:130:200]
[SET_BP_GROUP:BY_CATEGORY:THROAT]
[BP_APPEARANCE_MODIFIER:DEEP_VOICE:0:70:90:100:110:130:200]
[BP_APPEARANCE_MODIFIER:RASPY_VOICE:0:70:90:100:110:130:200]
[SET_BP_GROUP:BY_CATEGORY:HEAD]
[BP_APPEARANCE_MODIFIER:BROADNESS:90:95:98:100:102:105:110]
[APP_MOD_IMPORTANCE:700]
[APP_MOD_DESC_RANGE:91:94:98:102:106:109]
[BP_APPEARANCE_MODIFIER:HEIGHT:90:95:98:100:102:105:110]
[APP_MOD_IMPORTANCE:700]
[APP_MOD_DESC_RANGE:91:94:98:102:106:109]
[MAXAGE:50:105]
[ATTACK:PUNCH:BODYPART:BY_TYPE:GRASP]
[ATTACK_SKILL:GRASP_STRIKE]
[ATTACK_VERB:punch:punches]
[ATTACK_CONTACT_PERC:80]
[ATTACK_PREPARE_AND_RECOVER:3:3]
[ATTACK_FLAG_WITH]
[ATTACK_PRIORITY:SECOND]
[ATTACK:KICK:BODYPART:BY_TYPE:STANCE]
[ATTACK_SKILL:STANCE_STRIKE]
[ATTACK_VERB:kick:kicks]
[ATTACK_CONTACT_PERC:80]
[ATTACK_PREPARE_AND_RECOVER:4:4]
[ATTACK_FLAG_WITH]
[ATTACK_PRIORITY:SECOND]
[ATTACK_FLAG_BAD_MULTIATTACK]
[ATTACK:SCRATCH:CHILD_TISSUE_LAYER_GROUP:BY_TYPE:GRASP:BY_CATEGORY:FINGER:NAIL]
[ATTACK_SKILL:GRASP_STRIKE]
[ATTACK_VERB:slash:slashes]
[ATTACK_CONTACT_PERC:100]
[ATTACK_PENETRATION_PERC:150]
[ATTACK_FLAG_EDGE]
[ATTACK_PREPARE_AND_RECOVER:3:2]
[ATTACK_PRIORITY:MAIN]
[ATTACK:BITE:CHILD_BODYPART_GROUP:BY_CATEGORY:HEAD:BY_CATEGORY:TOOTH]
[ATTACK_SKILL:BITE]
[ATTACK_VERB:bite:bites]
[ATTACK_CONTACT_PERC:130]
[ATTACK_PENETRATION_PERC:100]
[ATTACK_FLAG_EDGE]
[ATTACK_PREPARE_AND_RECOVER:3:3]
[ATTACK_PRIORITY:SECOND]
[ATTACK_FLAG_CANLATCH]
[BABY:2]
[CHILD:14]
[EQUIPS]
[ALL_ACTIVE]
[SMELL_TRIGGER:90]
[HOMEOTHERM:10067]
[APPLY_CREATURE_VARIATION:STANDARD_BIPED_GAITS:900:675:450:225:1900:2900] 39 kph
[APPLY_CREATURE_VARIATION:STANDARD_CLIMBING_GAITS:6561:6115:5683:1755:7456:8567] 5 kph, NO DATA
[APPLY_CREATURE_VARIATION:STANDARD_SWIMMING_GAITS:5341:4723:4112:1254:6433:7900] 7 kph
[APPLY_CREATURE_VARIATION:STANDARD_CRAWLING_GAITS:2990:2257:1525:731:4300:6100] 12 kph, NO DATA
[SWIMS_INNATE]
[MANNERISM_FINGERS:finger:fingers]
[MANNERISM_NOSE:nose]
[MANNERISM_EAR:ear]
[MANNERISM_HEAD:head]
[MANNERISM_EYES:eyes]
[MANNERISM_MOUTH:mouth]
[MANNERISM_KNUCKLES:knuckles]
[MANNERISM_LIPS:lips]
[MANNERISM_CHEEK:cheek]
[MANNERISM_NAILS:nails]
[MANNERISM_FEET:feet]
[MANNERISM_ARMS:arms]
[MANNERISM_HANDS:hands]
[MANNERISM_TONGUE:tongue]
[MANNERISM_LEG:leg]
[MANNERISM_LAUGH]
[MANNERISM_SMILE]
[MANNERISM_WALK]
[MANNERISM_SIT]
[MANNERISM_BREATH]
[MANNERISM_POSTURE]
[MANNERISM_STRETCH]
[MANNERISM_EYELIDS]
[CASTE:FEMALE]
[FEMALE]
[MULTIPLE_LITTER_RARE]
[CASTE:MALE]
[MALE]
[SELECT_CASTE:ALL]
[SET_TL_GROUP:BY_CATEGORY:ALL:SCALE]
[TL_COLOR_MODIFIER:GREEN:4:MOSS_GREEN:3:MINT_GREEN:3:JADE:2:DARK_GREEN:2:TEAL:2:EMERALD:2:PINE_GREEN:1:AQUAMARINE:1]
[TLCM_NOUN:scales:PLURAL]
[SET_TL_GROUP:BY_CATEGORY:EYE:EYE]
[TL_COLOR_MODIFIER:RED:4:SCARLET:4:VERMILION:3:CHESTNUT:3:MAROON:2:DARK_SCARLET:2:PINK:1:FUCHSIA:1:CLEAR:1]
[TLCM_NOUN:eyes:PLURAL]
I believe only important change was the addition of LARGE_ROAMING, since it didn't start working until the final change I made, which was the addition of the line "[LARGE_ROAMING][DIFFICULTY:2][FREQUENCY:90] UBIQUITOUS ", and you already had a frequency. However, I didn't test a version with only that added, so it's possible it was a combination of the changes I made.
(Incidentally, this was done by comparing swamp monsters to river zoras from the zelda mod, which turned out to be very similar, and which do join civs)