The best answer to your questions would take time, time that I saddly lack at this moment of posting. You have ran into the nefarious issue of materials, tissues, and layering it.
You have materials and tissues you don't use
[BODY_DETAIL_PLAN:STANDARD_MATERIALS]
[BODY_DETAIL_PLAN:STANDARD_TISSUES]
this unfortunately is not layering anything right [BODY_DETAIL_PLAN:VERTEBRATE_TISSUE_LAYERS:CORTEX:NONE:NONE:PITH:NONE] if anything it's probably yelling errors in the log.
this is doing nothing? [SELECT_TISSUE_LAYER:ALL:BY_CATEGORY:TEN_ROOTS]
[SET_LAYER_TISSUE:CORTEX] I think?
[SET_TL_GROUP:BY_CATEGORY:ALL:SKIN]
[TL_COLOR_MODIFIER:BROWN:1]
[TLCM_NOUN:BARK:SINGULAR]
it has no skin (as above) it has CORTEX and PITH and the attacks passing though is an issue of unlayered limbs (as mentioned in the first line) Now since I can't better explain the fixes someone might be able to pick up and finish the correct way of getting this beast working. I will however post a creature similar to yours that I made from scratch so you can ref it and maybe figure out the fix on your own if noone or myself don't come back to help.
[CREATURE:MOLD_GRAY]
[DESCRIPTION:A horrific assembly of various creatures bones, animated by the will of sentient gray mold. Gray mold forms naturally in evil areas and have amazing healing abilities, but the decaying bodies they grow and feed on are consumed, the mold begins to nest inside the ribcage and take control of the skeleton. With a means of transport it enriches the bones with high amounts of calcium thickening them, the mold then hunts down living or dead and decaying bodies and attaches or attacks depending on the situation and devours them. Gray mold is very territorial and will even kill and absorb other weaker molds, some say they simply see which one is stronger and the loser joins with the stronger.]
[NAME:bone horror:bone horrors:gray mold]
[CASTE_NAME:bone horror:bone horrors:gray mold]
[CREATURE_TILE:'G'][COLOR:0:0:1]
[CAN_LEARN]
[NOPAIN][EXTRAVISION][NOBREATHE][NOSTUN][NONAUSEA][NOEMOTION]
[NOTHOUGHT][NOEXERT]
[NO_DIZZINESS]
[NO_FEVERS]
[LARGE_PREDATOR]
[NO_DRINK][NO_EAT][NO_SLEEP]
[OPPOSED_TO_LIFE][UBIQUITOUS]
[NOT_LIVING]
[NOFEAR]
[LARGE_ROAMING][DIFFICULTY:2]
[POPULATION_NUMBER:1000:2000]
[BIOME:SUBTERRANEAN_CHASM]
[UNDERGROUND_DEPTH:3:3]
[BENIGN][UBIQUITOUS][TRAPAVOID]
[PREFSTRING:constructed from various creatures bones]
[BODY_SIZE:0:0:280000]
[USE_MATERIAL_TEMPLATE:BONE:BONE_TEMPLATE]
[SHEAR_YIELD:155000]
[SHEAR_FRACTURE:310000]
[SHEAR_STRAIN_AT_YIELD:189] shear modulus 82 GPa
[MAX_EDGE:100000]
[BLOOD:LOCAL_CREATURE_MAT:BONE:SOLID]
[TISSUE:BONE]
[TISSUE_NAME:bone:bones] Whether it has a plural depends on exact part
[CONNECTIVE_TISSUE_ANCHOR]
[TISSUE_MATERIAL:LOCAL_CREATURE_MAT:BONE]
[RELATIVE_THICKNESS:50]
[HEALING_RATE:50]
[VASCULAR:3]
[CONNECTS]
[TISSUE_SHAPE:LAYER]
[TISSUE:MARROW]
[TISSUE_NAME:mold slime:NP] Whether it has a plural depends on exact part
[STRUCTURAL]
[FUNCTIONAL]
[CONNECTIVE_TISSUE_ANCHOR]
[TISSUE_MATERIAL:LOCAL_CREATURE_MAT:BONE]
[RELATIVE_THICKNESS:1]
[HEALING_RATE:100]
[VASCULAR:3]
[CONNECTS]
[TISSUE_SHAPE:LAYER]
[TISSUE:MOLD]
[TISSUE_NAME:slime:NP] Whether it has a plural depends on exact part
[FUNCTIONAL] --- this is for the THOUGHT which is what makes the killswitch work
[CONNECTIVE_TISSUE_ANCHOR]
[TISSUE_MATERIAL:LOCAL_CREATURE_MAT:BONE]
[RELATIVE_THICKNESS:1]
[HEALING_RATE:1]
[CONNECTS]
[TISSUE_SHAPE:LAYER]
[BODY:BONE_HORROR]
[TISSUE_LAYER:BY_CATEGORY:ALL:MARROW]
[BODY:SPINE:5FINGERS:MOUTH_SPLIT_JAW:TEETH:TAIL_2_PART:RIBCAGE]
[TISSUE_LAYER:BY_CATEGORY:ALL:BONE]
[TISSUE_LAYER:BY_CATEGORY:ALL:BONE]
[TISSUE_LAYER:BY_CATEGORY:ALL:BONE]
[BODY:MOLD_CORE]
[BODY_DETAIL_PLAN:BONE_HORROR_RIBCAGE_POSITIONS]
[TISSUE_LAYER:BY_CATEGORY:CORE:MOLD]
[BODY_APPEARANCE_MODIFIER:HEIGHT:75:95:98:100:102:105:125]
[APP_MOD_IMPORTANCE:500]
[BODY_APPEARANCE_MODIFIER:BROADNESS:75:95:98:100:102:105:125]
[APP_MOD_IMPORTANCE:500]
[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:180:180:180:180:180:180:180] for vampires
[APP_MOD_IMPORTANCE:1000]
[APP_MOD_NOUN:teeth:PLURAL]
[APP_MOD_DESC_RANGE:30:60:90:110:150:190]
[SET_BP_GROUP:BY_CATEGORY:HEAD]
[BP_APPEARANCE_MODIFIER:HIGH_CHEEKBONES: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]
[ATTACK:PUNCH:BODYPART:BY_TYPE:GRASP]
[ATTACK_SKILL:GRASP_STRIKE]
[ATTACK_VERB:punch:punches]
[ATTACK_CONTACT_PERC:100]
[ATTACK_VELOCITY_MODIFIER:3000]
[ATTACK_FLAG_WITH]
[ATTACK_PRIORITY:MAIN]
[ATTACK:PUNCH:BODYPART:BY_CATEGORY:JAW_HAND]
[ATTACK_SKILL:GRASP_STRIKE]
[ATTACK_VERB:slash:slashes]
[ATTACK_CONTACT_PERC:500]
[ATTACK_PENETRATION_PERC:200]
[ATTACK_VELOCITY_MODIFIER:3000]
[ATTACK_FLAG_EDGE]
[ATTACK_FLAG_WITH]
[ATTACK_PRIORITY:MAIN]
[ATTACK:PUNCH:BODYPART:BY_CATEGORY:TUSK_HAND]
[ATTACK_SKILL:GRASP_STRIKE]
[ATTACK_VERB:stab:stabs]
[ATTACK_CONTACT_PERC:50]
[ATTACK_PENETRATION_PERC:500]
[ATTACK_VELOCITY_MODIFIER:3000]
[ATTACK_FLAG_EDGE]
[ATTACK_FLAG_WITH]
[ATTACK_PRIORITY:MAIN]
[ATTACK:PUNCH:BODYPART:BY_CATEGORY:TAIL]
[ATTACK_SKILL:GRASP_STRIKE]
[ATTACK_VERB:whip:whips]
[ATTACK_CONTACT_PERC:200]
[ATTACK_VELOCITY_MODIFIER:3000]
[ATTACK_FLAG_WITH]
[ATTACK_PRIORITY:MAIN]
[ATTACK:PUNCH:BODYPART:BY_CATEGORY:TAIL_TIP]
[ATTACK_SKILL:GRASP_STRIKE]
[ATTACK_VERB:stab:stabs]
[ATTACK_CONTACT_PERC:50]
[ATTACK_PENETRATION_PERC:500]
[ATTACK_VELOCITY_MODIFIER:3000]
[ATTACK_FLAG_EDGE]
[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_VELOCITY_MODIFIER:3000]
[ATTACK_FLAG_WITH]
[ATTACK_PRIORITY:SECOND]
[ATTACK:SCRATCH:BODYPART:BY_CATEGORY:FINGER]
[ATTACK_SKILL:GRASP_STRIKE]
[ATTACK_VERB:scratch:scratches]
[ATTACK_CONTACT_PERC:100]
[ATTACK_PENETRATION_PERC:100]
[ATTACK_VELOCITY_MODIFIER:3000]
[ATTACK_FLAG_EDGE]
[ATTACK_PRIORITY:MAIN]
[ATTACK:BITE:BODYPART:BY_CATEGORY:MOUTH]
[ATTACK_SKILL:BITE]
[ATTACK_VERB:bite:bites]
[ATTACK_CONTACT_PERC:100]
[ATTACK_PENETRATION_PERC:100]
[ATTACK_VELOCITY_MODIFIER:3000]
[ATTACK_FLAG_EDGE]
[ATTACK_PRIORITY:MAIN]
[ATTACK_FLAG_CANLATCH]
[ATTACK:BITE:BODYPART:BY_CATEGORY:JAW]
[ATTACK_SKILL:BITE]
[ATTACK_VERB:bite:bites]
[ATTACK_CONTACT_PERC:100]
[ATTACK_PENETRATION_PERC:100]
[ATTACK_VELOCITY_MODIFIER:3000]
[ATTACK_FLAG_EDGE]
[ATTACK_PRIORITY:MAIN]
[ATTACK_FLAG_CANLATCH]
[DIURNAL]
[HOMEOTHERM:9999] --- not very warm
[SWIMS_LEARNED][SWIM_SPEED:2500]
[CASTE:GENERIC]
[SET_TL_GROUP:BY_CATEGORY:ALL:BONE]
[TL_COLOR_MODIFIER:WHITE:1:YELLOW:1]
[TLCM_NOUN:bones:PLURAL]
[ITEMCORPSE:TOOL:ITEM_TOOL_INGREDIENT:INORGANIC:MOLD_GRAY]