How can I change a controller's model at runtime without breaking mecanim?

I've got a gender select screen and based on this data, in the next scene, the character controller has a model/avatar assigned to it.

During testing I dragged and dropped a model/avatar onto the controller (male or female) and everything worked fine. However, when I assign the model/avatar 'on the fly' it doesn't work. The avatar just floats around.

I'm sure I'm missing something small but I don't know what it could be. Any help would be appreciated.

CODE:

     public GameObject MaleModel;
     public Avatar MaleAvatar;
     public GameObject FemaleModel;
     public Avatar FemaleAvatar;

     public GameObject Player;
 
     GameObject model;
     // Use this for initialization
     void Start () {
         int boy = PlayerPrefs.GetInt ("Gender");
 
         if (boy != 0) {
             model = Instantiate(MaleModel);
             Player.GetComponent<Animator>().avatar = MaleAvatar;
         } else {
             model = Instantiate(FemaleModel);
             Player.GetComponent<Animator>().avatar = FemaleAvatar;
         }
 
         model.transform.SetParent (Player.transform);
         model.transform.localPosition = new Vector3 (0, 0, 0);
     }