Deform Charater controler Collider acording to stance

I've been messing around with character controller and it's colliders

The idea is to deform the collision on the character when the characters changes stance (i.e stand, crouch, Prone etc.)

I've tried adding different colliders to the characters bones. but the character also makes use locomotion, so the rays casted from locomotion starts clashing with the colliders.

I've also tried scripting to the character controller to change size when the character changes stance, but with no results.

Any suggestion is appreciated. :)

I don't know if it will play well with locomotion or not, but I've tried it, and scripting the character controller collider DOES work... At least changing the height and center of the collider.

I created a small example project, but can't upload it here, so if you need it send me your email using a private message or something.

The code attached to my character controller:

using UnityEngine;
using System.Collections;

public class Crouch : MonoBehaviour 
{
    public  Transform           tHead;

    private Vector3             _v3InitialPosition;
    private Vector3             _v3CrouchingPosition;
    private CharacterController _characterController;
    private float               _fInitialControllerHeight;
    private float               _fCrouchingControllerHeight;
    private Vector3             _v3InitialControllerCenter;
    private Vector3             _v3CrouchingControllerCenter;

    void Start()
    {
        _v3InitialPosition = tHead.localPosition;
        _v3CrouchingPosition = _v3InitialPosition + Vector3.down;
        _characterController = GetComponent(typeof(CharacterController)) as CharacterController;
        _fInitialControllerHeight = _characterController.height;
        _fCrouchingControllerHeight = _fInitialControllerHeight - 1f;
        _v3InitialControllerCenter = _characterController.center;
        _v3CrouchingControllerCenter = _v3InitialControllerCenter + Vector3.down * 0.5f;
    }

    void Update () 
    {
        if (Input.GetKeyDown(KeyCode.Space))
        {
            tHead.localPosition = _v3CrouchingPosition;
            _characterController.height = _fCrouchingControllerHeight;
            _characterController.center = _v3CrouchingControllerCenter;
        }

        if (Input.GetKeyUp(KeyCode.Space))
        {
            tHead.localPosition = _v3InitialPosition;
            _characterController.height = _fInitialControllerHeight;
            _characterController.center = _v3InitialControllerCenter;
        }
    }
}