Custom model is horribly disfigured

The model, as far as I know, is perfectly fine, speaking for both QC and models, but when I compile it the MDL looks like an eldrich horror:
First one for hitboxes, second one for bones:

here’s the QC:


// Created by Crowbar 0.38.0.0

$ModelName "cookiecat\cookiecat.mdl"

$Model "cookieCat" "cookiecat.smd" {

	mouth 0 "mouth" "ValveBiped.Bip01_Head1" 0 1 0

	flexfile "cookiecat.vta" 
	{
		defaultflex frame 0
		flex "Mouth" frame 1
		flex "blink" frame 2
		flex "right_part" frame 1
	}

	flexcontroller phoneme range 0 1 blank
	flexcontroller mouth range 0 1 Mouth
	flexcontroller eyelid range 0 1 blink
	flexcontroller phoneme range 0 1 right_part

	localvar blank
	%blank = blank
	%Mouth = Mouth
	%blink = blink
	%right_part = right_part
}


$BodyGroup "Helmet"
{
	studio "helmet.smd"
	blank
}

$SurfaceProp "flesh"

$Contents "solid"

$CDMaterials "cookiecat\"

$Attachment "eyes" "ValveBiped.Bip01_Head1" 2.63 -4.13 0.04 rotate 0 -80.1 -90
$Attachment "mouth" "ValveBiped.Bip01_Head1" -0.2 -5.8 0 rotate 0 -80 -90
$Attachment "chest" "ValveBiped.Bip01_Spine2" 4 4 0 rotate 0 95 90
$Attachment "forward" "ValveBiped.forward" 0 0 0 rotate 0 0 0
$Attachment "anim_attachment_RH" "ValveBiped.Anim_Attachment_RH" 0 0 0 rotate -90 -90 0
$Attachment "anim_attachment_LH" "ValveBiped.Anim_Attachment_LH" 0 0 0 rotate -90 -90 0
$Attachment "anim_attachment_head" "ValveBiped.Bip01_Head1" 0 0 0 rotate -90 -90 0

$CBox 0 0 0 0 0 0

$BBox -14.374 -19.026 -0.141 13.44 19.026 50.537

$JiggleBone "tail_piece001" {
 is_flexible {
 yaw_stiffness 300
 yaw_damping 9
 pitch_stiffness 500
 pitch_damping 10
 length 2000
 tip_mass 0
 angle_constraint 10
 }
}

$JiggleBone "tail_piece002" {
 is_flexible {
 yaw_stiffness 500
 yaw_damping 9
 pitch_stiffness 750
 pitch_damping 10
 length 2000
 tip_mass 0
 angle_constraint 15
 }
}

$JiggleBone "tail_piece003" {
 is_flexible {
 yaw_stiffness 500
 yaw_damping 9
 pitch_stiffness 750
 pitch_damping 10
 length 2000
 tip_mass 0
 angle_constraint 15
 }
}

$includemodel "m_anm.mdl"

$definebone "ValveBiped.Bip01_Pelvis" "" -0.000005 1.830091 15.529095 -0.000000 0.000000 89.999983 0.000000 0.000000 0.000000 -0.000000 0.000000 0.000000
$definebone "ValveBiped.Bip01_Spine" "ValveBiped.Bip01_Pelvis" 0.000005 3.345126 -0.618196 4.943824 89.999983 89.999983 0.000000 0.000000 0.000000 -0.000000 -0.000000 0.000000
$definebone "ValveBiped.Bip01_Spine1" "ValveBiped.Bip01_Spine" 3.102871 -0.079216 0.000000 0.000000 -1.676188 0.000000 0.000000 0.000000 0.000000 0.000000 -0.000000 0.000000
$definebone "ValveBiped.Bip01_Spine2" "ValveBiped.Bip01_Spine1" 3.431019 -0.010136 0.000001 0.000000 5.749231 0.000000 0.000000 0.000000 0.000000 0.000000 -0.000000 0.000000
$definebone "ValveBiped.Bip01_Spine4" "ValveBiped.Bip01_Spine2" 3.190832 -0.087432 0.000002 -0.000000 11.120824 0.000000 0.000000 0.000000 0.000000 -0.000000 -0.000000 0.000000
$definebone "ValveBiped.Bip01_Neck1" "ValveBiped.Bip01_Spine4" 1.984459 0.239205 0.000000 0.000000 22.945930 179.999857 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
$definebone "ValveBiped.Bip01_Head1" "ValveBiped.Bip01_Neck1" 1.674675 0.439104 0.000002 -0.000057 23.296292 0.000000 0.000000 0.000000 0.000000 -0.000000 0.000000 0.000000
$definebone "ValveBiped.forward" "ValveBiped.Bip01_Head1" 1.999990 -3.000014 0.000001 -0.000000 -76.000329 -89.999928 0.000000 0.000000 0.000000 -0.000000 -0.000000 -0.000000
$definebone "ValveBiped.Bip01_R_Clavicle" "ValveBiped.Bip01_Spine4" 0.710543 1.239978 -1.937611 73.712202 168.619396 -95.595984 -0.000000 0.000000 -0.000000 -0.000000 0.000003 0.000001
$definebone "ValveBiped.Bip01_R_UpperArm" "ValveBiped.Bip01_R_Clavicle" 6.028141 -0.000008 -0.000016 -1.671748 -8.205610 93.355662 -0.000002 0.000000 0.000000 25.437872 -0.482168 -0.207112
$definebone "ValveBiped.Bip01_R_Forearm" "ValveBiped.Bip01_R_UpperArm" 6.084496 0.000000 0.000002 -8.742643 0.692630 0.955612 0.000001 0.000000 0.000000 16.695740 3.724229 1.071314
$definebone "ValveBiped.Bip01_R_Hand" "ValveBiped.Bip01_R_Forearm" 3.718539 -0.000000 0.000000 4.387831 -1.050400 -89.935520 0.000000 0.000000 0.000000 0.000000 0.000003 0.000001
$definebone "ValveBiped.Anim_Attachment_RH" "ValveBiped.Bip01_R_Hand" 2.676089 -1.712435 -0.001807 -0.010025 -105.017384 -90.037173 0.000000 0.000000 0.000000 -0.000003 0.000001 0.000000
$definebone "ValveBiped.Bip01_L_Clavicle" "ValveBiped.Bip01_Spine4" 0.710535 1.239972 1.937661 -73.711860 168.619273 91.480597 0.000000 0.000000 0.000000 -0.000000 0.000002 0.000000
$definebone "ValveBiped.Bip01_L_UpperArm" "ValveBiped.Bip01_L_Clavicle" 6.028144 0.000011 -0.000002 2.254616 -8.065833 -89.279221 0.000002 -0.000000 0.000002 -25.437748 -0.481783 0.206944
$definebone "ValveBiped.Bip01_L_Forearm" "ValveBiped.Bip01_L_UpperArm" 6.084498 0.000000 0.000000 8.743338 0.692770 -0.955625 0.000000 0.000000 0.000000 -16.694929 3.724374 -1.071308
$definebone "ValveBiped.Bip01_L_Hand" "ValveBiped.Bip01_L_Forearm" 3.718509 0.000000 0.000000 -4.388180 -1.175312 90.417560 0.000000 0.000000 0.000000 -0.000001 -0.000007 0.000000
$definebone "ValveBiped.Anim_Attachment_LH" "ValveBiped.Bip01_L_Hand" 2.676098 -1.712425 -0.004002 0.022288 74.985280 90.083120 0.000000 0.000000 0.000000 0.000002 0.000000 0.000000
$definebone "ValveBiped.Bip01_R_Thigh" "ValveBiped.Bip01_Pelvis" -5.640452 -1.893375 0.000007 1.549787 -98.008626 -90.398292 0.000000 0.000000 0.000000 7.706496 -1.406136 -0.188598
$definebone "ValveBiped.Bip01_R_Calf" "ValveBiped.Bip01_R_Thigh" 6.053804 0.000000 0.000000 -15.545195 -0.140642 0.678892 0.000000 0.000000 0.000000 -7.839081 -3.451070 0.471255
$definebone "ValveBiped.Bip01_R_Foot" "ValveBiped.Bip01_R_Calf" 6.965471 0.000000 0.000000 6.069684 -58.489882 -4.716734 0.000000 0.000000 0.000000 0.000000 -0.000002 0.000000
$definebone "ValveBiped.Bip01_L_Thigh" "ValveBiped.Bip01_Pelvis" 5.640451 -1.893383 -0.000003 1.548724 -81.991723 -89.601640 0.000001 -0.000000 -0.000000 -7.706287 -1.407140 0.188727
$definebone "ValveBiped.Bip01_L_Calf" "ValveBiped.Bip01_L_Thigh" 6.053801 0.000000 0.000000 15.545161 -0.138659 -0.678855 0.000000 0.000000 0.000000 7.839313 -3.450897 -0.471245
$definebone "ValveBiped.Bip01_L_Foot" "ValveBiped.Bip01_L_Calf" 6.965452 -0.000000 -0.000000 -6.069766 -58.490770 5.329819 -0.000000 0.000000 0.000000 0.000000 -0.000002 -0.000000
$definebone "tail_piece001" "ValveBiped.Bip01_Pelvis" 0.000000 0.915393 -9.702237 -0.000000 0.000000 -91.391470 0.000000 0.000000 0.000000 -0.000000 0.000000 0.000000
$definebone "tail_piece002" "tail_piece001" 0.000000 4.975285 -0.794355 -0.000000 0.000000 13.521116 0.000000 0.000000 0.000000 -0.000000 0.000000 0.000000
$definebone "tail_piece003" "tail_piece002" 0.000000 11.706352 2.208250 -0.000000 0.000000 77.870352 0.000000 0.000000 0.000000 -0.000000 0.000000 0.000000


$ikchain rhand "valvebiped.Bip01_R_Hand" Z 0 knee 0.7 0.707 0
$ikchain lhand "valvebiped.Bip01_L_Hand" Z 0 knee 0.7 0.707 0
$ikchain rfoot "valvebiped.Bip01_R_Foot" Z 0 knee 0.7 -0.707 0 pad 4
$ikchain lfoot "valvebiped.Bip01_L_Foot" Z 0 knee 0.7 -0.707 0 pad 4

$ikautoplaylock rhand 0.01 0
$ikautoplaylock lhand 0.01 0
$ikautoplaylock rfoot 0.05 0
$ikautoplaylock lfoot 0.05 0

$cmdlist lockfeet {
    ikrule lfoot footstep height 0 floor 0
    ikrule rfoot footstep height 0 floor 0
}

$cmdlist lockfeetandlefthand {
    ikrule lfoot footstep height 0 floor 0
    ikrule rfoot footstep height 0 floor 0
    ikrule lhand touch "ValveBiped.Bip01_R_Hand"
}

$cmdlist lockfeetnolefthand {
    ikrule lfoot footstep height 0 floor 0
    ikrule rfoot footstep height 0 floor 0
    ikrule lhand release
}

$cmdlist releasefeet {
    ikrule lfoot release
    ikrule rfoot release
}

$sequence reference "anims/reference.smd" fps 1
$animation a_proportions "anims/a_proportions.smd" subtract reference 0
$sequence proportions a_proportions predelta autoplay

$sequence "ragdoll" "anims\ragdoll.smd" {
fps 30
"ACT_DIERAGDOLL" 1
}

$CollisionJoints "physics.smd"
{
	$mass 20.5
	$inertia 10
	$damping 0
	$rotdamping 4
	$rootbone "ValveBiped.Bip01_Pelvis"


	$jointconstrain "ValveBiped.Bip01_Spine4" x limit -15 15 0
	$jointconstrain "ValveBiped.Bip01_Spine4" y limit -30 30 0
	$jointconstrain "ValveBiped.Bip01_Spine4" z limit -30 30 0

	$jointconstrain "ValveBiped.Bip01_Head1" x limit -15 15 0
	$jointconstrain "ValveBiped.Bip01_Head1" y limit -30 30 0
	$jointconstrain "ValveBiped.Bip01_Head1" z limit -30 30 0

	$jointconstrain "ValveBiped.Bip01_L_Forearm" x limit -30 30 0
	$jointconstrain "ValveBiped.Bip01_L_Forearm" y limit -90 90 0
	$jointconstrain "ValveBiped.Bip01_L_Forearm" z limit -45 45 0

	$jointconstrain "ValveBiped.Bip01_L_Hand" x limit 0 0 0
	$jointconstrain "ValveBiped.Bip01_L_Hand" y limit -30 30 0
	$jointconstrain "ValveBiped.Bip01_L_Hand" z limit -60 60 0

	$jointconstrain "ValveBiped.Bip01_R_Forearm" x limit -30 30 0
	$jointconstrain "ValveBiped.Bip01_R_Forearm" y limit -90 90 0
	$jointconstrain "ValveBiped.Bip01_R_Forearm" z limit -45 45 0

	$jointconstrain "ValveBiped.Bip01_R_Hand" x limit 0 0 0
	$jointconstrain "ValveBiped.Bip01_R_Hand" y limit -30 30 0
	$jointconstrain "ValveBiped.Bip01_R_Hand" z limit -60 60 0

	$jointconstrain "ValveBiped.Bip01_L_Thigh" x limit -30 30 0
	$jointconstrain "ValveBiped.Bip01_L_Thigh" y limit -60 60 0
	$jointconstrain "ValveBiped.Bip01_L_Thigh" z limit -10 55 0

	$jointconstrain "ValveBiped.Bip01_L_Calf" x limit 0 0 0
	$jointconstrain "ValveBiped.Bip01_L_Calf" y limit -10 90 0
	$jointconstrain "ValveBiped.Bip01_L_Calf" z limit 0 0 0

	$jointconstrain "ValveBiped.Bip01_R_Thigh" x limit -30 30 0
	$jointconstrain "ValveBiped.Bip01_R_Thigh" y limit -60 60 0
	$jointconstrain "ValveBiped.Bip01_R_Thigh" z limit -55 10 0

	$jointconstrain "ValveBiped.Bip01_R_Calf" x limit 0 0 0
	$jointconstrain "ValveBiped.Bip01_R_Calf" y limit -10 90 0
	$jointconstrain "ValveBiped.Bip01_R_Calf" z limit 0 0 0

}

and if needed, to see how it should be, here’s the blend file for both the reference, and the physics:
http://pasteall.org/blend/index.php?id=47790
http://pasteall.org/blend/index.php?id=47791

Texture for the helmet, which is a bodygroup, seems fine (as fine as purple and black can be), what’s worrying me is how the body has no texture at all, it’s invisible, other than that, the bones seem to be placed randomly, albeit, in order.