I hope a Stretch To constraint expert will find the smart way to fix your problem but from what I understand:
If you activate this armature layer you'll see some highly stretched bones:
These bones have a Stretch To constraint. You've probably scaled and applied the scale of your armature. This operation has stretched these bones, as the constraints have kept the same Original Length value but now the scale is not the same:
To bring the bones back to their good length you need to multiply the Original Length value by the previous armature scale, but you may not have it. Another way to fix it is to take note of the Target of the constraint, remove the constraint, then create a new one, and type the same Target, it will bring back the good Original Length value. If all your stretch bones have the same length then you could simply type this value in all your constraints instead of removing them.
If you have a previous version of your armature and character, you could avoid to apply the scale, or parent the armature to an empty and scale the empty itself, not the armature.