Your creature file is a little bit disjointed, keep it all together with the correct syntax. Off the bat if you're making a new creature file it might just be easier to insert them into
creature_standard for the time being if you've written the file down incorrectly and confused the system trying to read a new creature file.
I notice you've copied ontop of the dwarf raws, which is a dicey thing to do over writing fresh ones yourself (also because dwarves are kind of OP)
[CREATURE:ELEMENTMAN_GEM]
[LOCAL_POPS_PRODUCE_HEROES] <- to create occupational adventurers // optional suggestion by me
[LOCAL_POPS_CONTROLLABLE] <- To enable you to select them in adventure mode (as the playable civ, outsider_controllable needed elsewise ) //optional suggestion by me
[DESCRIPTION:A strange crystalline creature the shape of a human.]
[NAME:crystal man:crystal men:crystal man]
[CREATURE_TILE:'M']
[NOBONES][NOPAIN][NOBREATHE] <- stacking tags is egible, doesn't need to be a connection between them, but done here to save space
[NONAUSEA][NOSTUN][NOEXERT]
[NO_DIZZINESS][NOFEAR][NO_FEVERS]
[EXTRAVISION]
[NO_DRINK][NO_EAT]
[NOT_LIVING][NO_SLEEP]
[INTELLIGENT]
[STRANGE_MOODS][TRANCES]
[BENIGN]
[CANOPENDOORS]
[EQUIPS]
[NOT_BUTCHERABLE]
[ODOR_LEVEL:0]
[SMELL_TRIGGER:10000]
[PREFSTRING:rockiness]
[PROFESSION_NAME:CRAFTSMAN:craftsgem:craftsgems]
[PROFESSION_NAME:FISHERMAN:fishergem:fishergems]
[PROFESSION_NAME:HAMMERMAN:hammergem:hammergems]
[PROFESSION_NAME:SPEARMAN:speargem:speargems]
[PROFESSION_NAME:CROSSBOWMAN:marksgem:marksgems]
[PROFESSION_NAME:AXEMAN:axegem:axegems]
[PROFESSION_NAME:SWORDSMAN:swordsgem:swordsgems]
[PROFESSION_NAME:MACEMAN:macegem:macegems]
[PROFESSION_NAME:PIKEMAN:pikegem:pikegems]
[PROFESSION_NAME:BOWMAN:bowgem:bowgems]
[PROFESSION_NAME:MASTER_CROSSBOWMAN:Elite Marksgem:Elite Marksgems]
[PROFESSION_NAME:MASTER_BOWMAN:Elite Bowgem:Elite Bowgems]
[SPEECH:dwarf.txt]
[APPLY_CREATURE_VARIATION:STANDARD_BIPED_GAITS:900:711:521:293:1900:2900] 30 kph
[APPLY_CREATURE_VARIATION:STANDARD_CLIMBING_GAITS:5951:5419:4898:1463:6944:8233] 6 kph
[APPLY_CREATURE_VARIATION:STANDARD_SWIMMING_GAITS:5951:5419:4898:1463:6944:8233] 6 kph
[APPLY_CREATURE_VARIATION:STANDARD_CRAWLING_GAITS:2990:2257:1525:731:4300:6100] 12 kph
[SWIMS_LEARNED]
[PERSONALITY:IMMODERATION:0:55:100]
[PERSONALITY:STRESS_VULNERABILITY:0:45:100]
[PERSONALITY:BASHFUL:0:45:100]
[PERSONALITY:SINGLEMINDED:0:55:100]
[PERSONALITY:GREED:0:55:100]
[MANNERISM_HEAD:head]
[MANNERISM_FEET:feet]
[MANNERISM_ARMS:arms]
[MANNERISM_HANDS:hands]
[MANNERISM_LEG:leg]
[MANNERISM_LAUGH]
[MANNERISM_SMILE]
[MANNERISM_WALK]
[MANNERISM_SIT]
[MANNERISM_POSTURE]
[GAIT:WALK:Sprint:351:10:3:730:50:LAYERS_SLOW:STRENGTH:AGILITY:STEALTH_SLOWS:50]
[GAIT:WALK:Run:561:5:3:730:10:LAYERS_SLOW:STRENGTH:AGILITY:STEALTH_SLOWS:20]
[GAIT:WALK:Jog:730:NO_BUILD_UP:5:LAYERS_SLOW:STRENGTH:AGILITY:STEALTH_SLOWS:10]
[GAIT:WALK:Walk:900:NO_BUILD_UP:0]
[GAIT:WALK:Stroll:1900:NO_BUILD_UP:0]
[GAIT:WALK:Creep:2900:NO_BUILD_UP:0]
[GAIT:CLIMB:Scramble:731:10:3:2257:50:LAYERS_SLOW:STRENGTH:AGILITY:STEALTH_SLOWS:50]
[GAIT:CLIMB:Faster Climb:1525:5:3:2257:10:LAYERS_SLOW:STRENGTH:AGILITY:STEALTH_SLOWS:20]
[GAIT:CLIMB:Fast Climb:2257:NO_BUILD_UP:5:LAYERS_SLOW:STRENGTH:AGILITY:STEALTH_SLOWS:10]
[GAIT:CLIMB:Climb:2990:NO_BUILD_UP:0]
[GAIT:CLIMB:Slow Climb:4300:NO_BUILD_UP:0]
[GAIT:CLIMB:Creep:6100:NO_BUILD_UP:0]
[GAIT:CRAWL:Scramble:731:10:3:2257:50:LAYERS_SLOW:STRENGTH:AGILITY:STEALTH_SLOWS:50]
[GAIT:CRAWL:Faster Crawl:1525:5:3:2257:10:LAYERS_SLOW:STRENGTH:AGILITY:STEALTH_SLOWS:20]
[GAIT:CRAWL:Fast Crawl:2257:NO_BUILD_UP:5:LAYERS_SLOW:STRENGTH:AGILITY:STEALTH_SLOWS:10]
[GAIT:CRAWL:Crawl:2990:NO_BUILD_UP:0]
[GAIT:CRAWL:Slow Crawl:4300:NO_BUILD_UP:0]
[GAIT:CRAWL:Creep:6100:NO_BUILD_UP:0]
[BODY:HUMANOID_SIMPLE]
[NO_THOUGHT_CENTER_FOR_MOVEMENT]
[CASTE:AMETHYST]
[CASTE_NAME:amethyst woman:amethyst women:amethyst woman]
[FEMALE]
[MULTIPLE_LITTER_RARE]
[TISSUE:ROCK]
[TISSUE_NAME:amethyst:NP]
[TISSUE_MATERIAL:INORGANIC:AMETHYST]
[MUSCULAR]
[FUNCTIONAL]
[STRUCTURAL]
[RELATIVE_THICKNESS:1]
[CONNECTS]
[TISSUE_SHAPE:LAYER]
[TISSUE_LAYER:BY_CATEGORY:ALL:ROCK]
[ITEMCORPSE:ROUGH:NO_SUBTYPE:INORGANIC:AMETHYST]
[COLOR:5:0:1]
[CASTE:ONYX]
[CASTE_NAME:onyx man:onyx men:onyx man]
[MALE]
[TISSUE:ROCK]
[TISSUE_NAME:onyx:NP]
[TISSUE_MATERIAL:INORGANIC:ONYX]
[MUSCULAR]
[FUNCTIONAL]
[STRUCTURAL]
[RELATIVE_THICKNESS:1]
[CONNECTS]
[TISSUE_SHAPE:LAYER]
[TISSUE_LAYER:BY_CATEGORY:ALL:ROCK]
[ITEMCORPSE:ROUGH:NO_SUBTYPE:INORGANIC:ONYX]
[COLOR:0:0:1]
[SELECT_CASTE:ALL]
[BODY_SIZE:0:0:70000] < - Don't define separately if they are the same
[BODY_APPEARANCE_MODIFIER:HEIGHT:90:95:98:100:102:105:110]
[BODY_APPEARANCE_MODIFIER:BROADNESS:90:95:98:100:102:105:110]
[ATTACK:PUNCH:BODYPART:BY_TYPE:GRASP]
[ATTACK_SKILL:GRASP_STRIKE]
[ATTACK_VERB:punch:punches]
[ATTACK_CONTACT_PERC:100]
[ATTACK_PREPARE_AND_RECOVER:3:3]
[ATTACK_FLAG_WITH]
[ATTACK_PRIORITY:MAIN]
[ATTACK:KICK:BODYPART:BY_TYPE:STANCE]
[ATTACK_SKILL:STANCE_STRIKE]
[ATTACK_VERB:kick:kicks]
[ATTACK_CONTACT_PERC:100]
[ATTACK_PREPARE_AND_RECOVER:4:4]
[ATTACK_FLAG_WITH]
[ATTACK_PRIORITY:SECOND]
[ATTACK_FLAG_BAD_MULTIATTACK]
[ALL_ACTIVE]
Can you show us your entity entry? Besides from the possibly faulty creature file (someone else will need to chip in and tell both of us whether your effort to port it to its own file was correctly done) the creature looks ok, i've made some small alterations to syntax that should make it correct.
You never gave them a [BODY]. You want to do that before defining any tissues, so near the start where it is with most creature files. Also there's no need to use the [CASTE] token to define a caste and then use [SELECT_CASTE] to select it. When you first define a caste it's already selected.
They gave it [BODY:HUMANOID_SIMPLE] which is the same template used for grimelings, but they are right that [SELECT_CASTE] isn't nessecary until you stop talking about the caste and say [SELECT_CASTE:ALL] to resume the file, and i've made some mid-writing edits to my code fix for you.
Hold the phones, i've found another issue, they don't have a universal body-height & both the castes are identically matched, doesn't need to be defined seperately to the caste if it applies to all, edited the fix respectively [BODY_SIZE:0:0:70000]
[BODY_APPEARANCE_MODIFIER:HEIGHT:90:95:98:100:102:105:110]
[BODY_APPEARANCE_MODIFIER:BROADNESS:90:95:98:100:102:105:110]