Ok there are many thing that are wrong here, I'll try to cover everything.
First, you must define body parts only one time for each caste. With this line:[BODY:HUMANOID:2EYES:2EARS:NOSE:2LUNGS:HEART:GUTS:ORGANS:HUMANOID_JOINTS:THROAT:NECK:SPINE:BRAIN:SKULL:5FINGERS:5TOES:MOUTH:TONGUE:FACIAL_FEATURES:TEETH:RIBCAGE]
you say that every caste will have this body. When you put it a second time after the caste, you create 'fractal spacemarines' with heads and legs and hands everywhere (basically if you look at it in the Arena, it has multiples body parts that should not be here). What you want to do is define the body only after the caste is declared.
Take a look at this:[CREATURE:SKELETONS]
[DESCRIPTION:The skeleton of an ancient warrior. It has no master and his only animated by his hatred for all living being.]
[NAME:skeleton:skeletons:skeleton]
[CREATURE_TILE:'U'][COLOR:7:0:1]
[NOT_LIVING]
[OPPOSED_TO_LIFE]
[SMELL_TRIGGER:10000]
[ODOR_LEVEL:10]
[NOT_BUTCHERABLE]
[PREFSTRING:pale bones]
[LARGE_ROAMING]
[EVIL]
[BIOME:ANY_WETLAND]
[BIOME:SUBTERRANEAN_CHASM]
[UNDERGROUND_DEPTH:2:3]
[CLUSTER_NUMBER:1:3]
[POPULATION_NUMBER:10:30]
[NOBONES]
[NOPAIN][EXTRAVISION][NOBREATHE][NOSTUN][NONAUSEA][NOEMOTION][NOTHOUGHT][NOEXERT]
[NO_DIZZINESS]
[LARGE_PREDATOR]
[NO_DRINK][NO_EAT][NO_SLEEP]
[CANOPENDOORS]
[NOFEAR]
[CREATURE_CLASS:SKELETON]
[ALL_ACTIVE]
[NO_THOUGHT_CENTER_FOR_MOVEMENT]
[USE_MATERIAL_TEMPLATE:STRONG_BONE:BONE_STRONG_TEMPLATE]
[USE_MATERIAL_TEMPLATE:BONE:BONE_TEMPLATE]
[TISSUE:STRONG_BONE]
[TISSUE_NAME:bone:NP]
[TISSUE_MATERIAL:LOCAL_CREATURE_MAT:STRONG_BONE]
[MUSCULAR]
[FUNCTIONAL]
[STRUCTURAL]
[RELATIVE_THICKNESS:1]
[CONNECTS]
[TISSUE_SHAPE:LAYER]
[TISSUE:BONE]
[TISSUE_NAME:bone:NP]
[TISSUE_MATERIAL:LOCAL_CREATURE_MAT:BONE]
[MUSCULAR]
[FUNCTIONAL]
[STRUCTURAL]
[RELATIVE_THICKNESS:1]
[CONNECTS]
[TISSUE_SHAPE:LAYER]
[TISSUE:METAL]
[TISSUE_NAME:iron:NP]
[TISSUE_MATERIAL:INORGANIC:IRON]
[CONNECTS]
[RELATIVE_THICKNESS:10]
[TISSUE_SHAPE:LAYER]
[CASTE:GIANT_SKELETON]
[BODY:HUMANOID_ARMLESS:ARMS_WITHOUT_GRASP:HUMANOID_JOINTS:SPINE:5FINGERS_HOLDING:5TOES:MOUTH:TEETH:RIBCAGE:GREATWEAPON_RIGHT]
[CASTE:SWORD_SKELETON]
[BODY:HUMANOID_ARMLESS:ARMS_ONE_GRASP:HUMANOID_JOINTS:SPINE:5FINGERS_HOLDING:5TOES:MOUTH:TEETH:RIBCAGE:GREATWEAPON_RIGHT]
[CASTE:ARCHER_SKELETON]
[BODY:HUMANOID:HUMANOID_JOINTS:SPINE:5FINGERS:5TOES:MOUTH:TEETH:RIBCAGE]
[CASTE:BABY_SKELETON]
[BODY:HUMANOID:HUMANOID_JOINTS:SPINE:5FINGERS:5TOES:MOUTH:TEETH:RIBCAGE]
[CASTE:BEAST_SKELETON]
[BODY:QUADRUPED:TAIL:SPINE:4TOES_FQ_REG:4TOES_RQ_REG:MOUTH:GENERIC_TEETH_WITH_LARGE_EYE_TEETH:RIBCAGE]
[CASTE:WHEEL_SKELETON]
[BODY:HUMANOID_ARMLESS:ARMS_WITHOUT_GRASP:HUMANOID_JOINTS:SPINE:5FINGERS_HOLDING:5TOES:MOUTH:TEETH:RIBCAGE:WHEEL]
[CASTE:BONE_TOWER]
[BODY:BASIC_2PARTBODY:HANDS_TOWER]
[SELECT_CASTE:ALL]
[BODYGLOSS:SKULL]
[TISSUE_LAYER:BY_CATEGORY:GREATWEAPON:METAL]
[SELECT_CASTE:GIANT_SKELETON]
[SELECT_ADDITIONAL_CASTE:BEAST_SKELETON]
[BODY_DETAIL_PLAN:SKELETON_LAYER:STRONG_BONE]
[SELECT_CASTE:GIANT_SKELETON]
[DESCRIPTION:A giant skeleton animated by death magic and wielding a great sword. It may be slow, but it's swings are devastatings.]
[CASTE_NAME:giant skeleton:giants skeletons:giant skeleton]
[CASTE_TILE:'S'][COLOR:7:0:1]
[BODYGLOSS:GREATSWORD]
[BODY_SIZE:0:0:240000]
[NATURAL_SKILL:SWORD:6]
[NATURAL_SKILL:MELEE_COMBAT:5]
[NATURAL_SKILL:DODGING:5]
[NATURAL_SKILL:SITUATIONAL_AWARENESS:7]
[ATTACK:KICK:BODYPART:BY_TYPE:STANCE]
[ATTACK_SKILL:STANCE_STRIKE]
[ATTACK_VERB:kick:kicks]
[ATTACK_PREPARE_AND_RECOVER:4:4]
[ATTACK_FLAG_BAD_MULTIATTACK]
[ATTACK_CONTACT_PERC:100]
[ATTACK_FLAG_WITH]
[ATTACK_PRIORITY:SECOND]
[ATTACK:SLASH:BODYPART:BY_CATEGORY:GREATWEAPON]
[ATTACK_SKILL:SWORD]
[ATTACK_VERB:slash:slashes]
[ATTACK_PREPARE_AND_RECOVER:4:3]
[ATTACK_CONTACT_PERC:250]
[ATTACK_PENETRATION_PERC:850]
[ATTACK_FLAG_EDGE]
[ATTACK_FLAG_WITH]
[ATTACK_PRIORITY:MAIN]
[ATTACK:CRUSH:BODYPART:BY_CATEGORY:GREATWEAPON]
[ATTACK_SKILL:SWORD]
[ATTACK_VERB:crush:crushes]
[ATTACK_PREPARE_AND_RECOVER:5:3]
[ATTACK_CONTACT_PERC:90]
[ATTACK_PENETRATION_PERC:2000]
[ATTACK_VELOCITY_MODIFIER:400]
[ATTACK_FLAG_EDGE]
[ATTACK_FLAG_WITH]
[ATTACK_PRIORITY:MAIN]
[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
[SELECT_CASTE:BEAST_SKELETON]
[DESCRIPTION:A giant quadruped beast with an human head.]
[CASTE_NAME:skeleton beast:skeleton beasts:skeleton beast]
[CASTE_TILE:'B'][COLOR:7:0:1]
[BODY_SIZE:0:0:350000]
[NATURAL_SKILL:BITE:7]
[NATURAL_SKILL:STANCE_STRIKE:6]
[NATURAL_SKILL:DODGING:5]
[NATURAL_SKILL:SITUATIONAL_AWARENESS:7]
[ATTACK:KICK:BODYPART:BY_CATEGORY:LEG_FRONT]
[ATTACK_SKILL:STANCE_STRIKE]
[ATTACK_VERB:swipe:swipes]
[ATTACK_PREPARE_AND_RECOVER:3:3]
[ATTACK_FLAG_BAD_MULTIATTACK]
[ATTACK_CONTACT_PERC:80]
[ATTACK_FLAG_WITH]
[ATTACK_PRIORITY:MAIN]
[ATTACK:BITE:CHILD_BODYPART_GROUP:BY_CATEGORY:HEAD:BY_CATEGORY:TOOTH]
[ATTACK_SKILL:BITE]
[ATTACK_VERB:bite:bite]
[ATTACK_PREPARE_AND_RECOVER:3:3]
[ATTACK_CONTACT_PERC:100]
[ATTACK_PENETRATION_PERC:80]
[ATTACK_FLAG_EDGE]
[ATTACK_FLAG_CANLATCH]
[ATTACK_PRIORITY:SECOND]
[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
[SELECT_CASTE:SWORD_SKELETON]
[SELECT_ADDITIONAL_CASTE:ARCHER_SKELETON]
[SELECT_ADDITIONAL_CASTE:BONE_TOWER]
[SELECT_ADDITIONAL_CASTE:BABY_SKELETON]
[SELECT_ADDITIONAL_CASTE:WHEEL_SKELETON]
[BODY_DETAIL_PLAN:SKELETON_LAYER:BONE]
[SELECT_CASTE:SWORD_SKELETON]
[DESCRIPTION:A skeleton animated by death magic and wielding a scimitar.]
[CASTE_NAME:skeleton:skeletons:skeleton]
[CASTE_TILE:'s'][COLOR:7:0:1]
[BODYGLOSS:SCIMITAR]
[BODY_SIZE:0:0:65000]
[NATURAL_SKILL:MELEE_COMBAT:3]
[NATURAL_SKILL:SWORD:4]
[NATURAL_SKILL:DODGING:3]
[NATURAL_SKILL:SITUATIONAL_AWARENESS:5]
[ATTACK:KICK:BODYPART:BY_TYPE:STANCE]
[ATTACK_SKILL:STANCE_STRIKE]
[ATTACK_VERB:kick:kicks]
[ATTACK_PREPARE_AND_RECOVER:3:3]
[ATTACK_FLAG_BAD_MULTIATTACK]
[ATTACK_CONTACT_PERC:100]
[ATTACK_FLAG_WITH]
[ATTACK_PRIORITY:SECOND]
[ATTACK:SLASH:BODYPART:BY_CATEGORY:GREATWEAPON]
[ATTACK_SKILL:SWORD]
[ATTACK_VERB:slash:slashes]
[ATTACK_PREPARE_AND_RECOVER:2:2]
[ATTACK_CONTACT_PERC:200]
[ATTACK_PENETRATION_PERC:600]
[ATTACK_FLAG_EDGE]
[ATTACK_FLAG_WITH]
[ATTACK_PRIORITY:MAIN]
[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
[SELECT_CASTE:ARCHER_SKELETON]
[DESCRIPTION:A skeleton animated by death magic.]
[CASTE_NAME:skeleton:skeletons:skeleton]
[CASTE_TILE:'s'][COLOR:7:0:1]
[NATURAL_SKILL:MELEE_COMBAT:3]
[NATURAL_SKILL:RANGED_COMBAT:4]
[NATURAL_SKILL:BOW:5]
[NATURAL_SKILL:DODGING:3]
[NATURAL_SKILL:SITUATIONAL_AWARENESS:6]
[BODY_SIZE:0:0:65000]
[ATTACK:KICK:BODYPART:BY_TYPE:STANCE]
[ATTACK_SKILL:STANCE_STRIKE]
[ATTACK_VERB:kick:kicks]
[ATTACK_PREPARE_AND_RECOVER:3:3]
[ATTACK_FLAG_BAD_MULTIATTACK]
[ATTACK_CONTACT_PERC:100]
[ATTACK_FLAG_WITH]
[ATTACK_PRIORITY:MAIN]
[ATTACK:PUNCH:BODYPART:BY_TYPE:GRASP]
[ATTACK_SKILL:GRASP_STRIKE]
[ATTACK_VERB:punch:punches]
[ATTACK_PREPARE_AND_RECOVER:3:3]
[ATTACK_CONTACT_PERC:100]
[ATTACK_FLAG_WITH]
[ATTACK_PRIORITY:MAIN]
[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
[SELECT_CASTE:BONE_TOWER]
[DESCRIPTION:A grim tower made from the bones of the fallen.]
[CASTE_NAME:bone tower:bone towers:bone tower]
[CASTE_TILE:'T'][COLOR:7:0:1]
[BODYGLOSS]
[NATURAL_SKILL:MELEE_COMBAT:4]
[NATURAL_SKILL:GRASP_STRIKE:5]
[NATURAL_SKILL:STANCE_STRIKE:5]
[NATURAL_SKILL:SITUATIONAL_AWARENESS:6]
[BODY_SIZE:0:0:600000]
[ATTACK:SLAM:BODYPART:BY_CATEGORY:BODY_UPPER]
[ATTACK_SKILL:STANCE_STRIKE]
[ATTACK_VERB:slam:slams]
[ATTACK_PREPARE_AND_RECOVER:3:3]
[ATTACK_FLAG_BAD_MULTIATTACK]
[ATTACK_CONTACT_PERC:100]
[ATTACK_FLAG_WITH]
[ATTACK_PRIORITY:SECOND]
[ATTACK:PUNCH:BODYPART:BY_TYPE:GRASP]
[ATTACK_SKILL:GRASP_STRIKE]
[ATTACK_VERB:punch:punches]
[ATTACK_PREPARE_AND_RECOVER:3:3]
[ATTACK_FLAG_INDEPENDENT_MULTIATTACK]
[ATTACK_CONTACT_PERC:100]
[ATTACK_FLAG_WITH]
[ATTACK_PRIORITY:MAIN]
[APPLY_CREATURE_VARIATION:STANDARD_CRAWLING_GAITS::3512:2634:1756:878:4900:6900] 10 kph
[CANNOT_CLIMB][SWIMS_LEARNED]
[SELECT_CASTE:BABY_SKELETON]
[DESCRIPTION:A tiny skeleton which seems to be the one of an infant. Despite it's size, it is an enraged foe.]
[CASTE_NAME:baby skeleton:baby skeletons:baby skeleton]
[CASTE_TILE:'b'][COLOR:7:0:1]
[BODY_SIZE:0:0:4000]
[PRONE_TO_RAGE:60]
[ATTACK:BITE:CHILD_BODYPART_GROUP:BY_CATEGORY:HEAD:BY_CATEGORY:TOOTH]
[ATTACK_SKILL:BITE]
[ATTACK_VERB:bite:bites]
[ATTACK_CONTACT_PERC:100]
[ATTACK_PENETRATION_PERC:100]
[ATTACK_FLAG_CANLATCH]
[ATTACK_FLAG_EDGE]
[ATTACK_PREPARE_AND_RECOVER:3:3]
[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
[SELECT_CASTE:WHEEL_SKELETON]
[DESCRIPTION:A skeleton animated by death magic.]
[CASTE_NAME:wheel skeleton:wheel skeletons:skeleton]
[CASTE_TILE:'s'][COLOR:7:0:1]
[BODY_SIZE:0:0:65000]
[NATURAL_SKILL:MELEE_COMBAT:4]
[NATURAL_SKILL:STANCE_STRIKE:5]
[NATURAL_SKILL:DODGING:3]
[NATURAL_SKILL:SITUATIONAL_AWARENESS:5]
[TISSUE_LAYER:BY_CATEGORY:WHEEL:METAL]
[ATTACK:RUSH:BODYPART:BY_CATEGORY:WHEEL]
[ATTACK_SKILL:STANCE_STRIKE]
[ATTACK_VERB:roll toward:rolls toward]
[ATTACK_PREPARE_AND_RECOVER:2:2]
[ATTACK_CONTACT_PERC:300]
[ATTACK_PENETRATION_PERC:705]
[ATTACK_FLAG_EDGE]
[ATTACK_FLAG_WITH]
[ATTACK_PRIORITY:MAIN]
[GAIT:WALK:Roll:160:2:3:700:0]
[GAIT:WALK:Run:450:5:3:711:10:LAYERS_SLOW:STRENGTH:AGILITY:STEALTH_SLOWS:20]
[GAIT:WALK:Walk:900:NO_BUILD_UP:0]
[GAIT:WALK:Creep:2900:NO_BUILD_UP:0]
[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
See how the difference between the caste are handled ? It's what you want to do.
The same thing is true for everything before your first caste. You define variations, attacks and names which affect all of the caste but are pointless in the case of your tank. You should move them after the [caste] token.
[SWIM_SPEED] doesn't exists anymore, it's replaced by the GAITS tokens. Look at the humans raws in vanilla(or the example I gave you).
Also you may want to put a [DESCRIPTION] and a [CASTE_NAME] after the caste because right now it's difficult to say who is what.
And your tanks are fine, the ones that are burning are the fleshy ones.