Delay jump problem

Hello everyone,
I have a problem with the character controller included in FPS controller.

My character has an animation for a jump that make him crouch a little bit before really jumping. In the FPSInputController script, I delayed the jump correctly, but my problem is the animation … My character is now crouching for about 0.2 seconds and is not touching the floor because of the capsule collider (still on the floor). After this time, the characte really jumps with its capsule collider. A possibility should be to move the center of the capsule collider threw time to have a fluid animation and my foot still on the ground. I don’t have any clue to do that …

An other possibility could be to not use this character controller, and have a rigidbody collider on my character, but I must to everything from scratch to be able to move my character …
I saw this topic, very interesting :
http://answers.unity3d.com/questions/7671/guidelines-for-using-rigidbody-collider-characterc.html
But I still don’t know what should be the best to do.

So my question is, can it be done with the capsule collider of the character controller, or should I start to do from scratch all this ? (quite not my favourite answer :o( ).

you can easily modify the center of your capsule:

function ModifyCCCenter(){
    var controller : CharacterController;
    controller = GetComponent(CharacterController);
    controller.center = Vector3 (0, 1, 0);
}

Put this on a script attahced to your obejct and use animation event you can easily add
http://docs.unity3d.com/Documentation/Components/animeditor-AnimationEvents.html

Same reverse process to put it back to normal.