How to use an array to set path by instantiating nodes?

I have a GameObject which for now is just a cube. What I am trying to do is to get the cube to follow a path that I create in real time by clicking in the game world.

I have an array set up which, once instantiated, each waypoint is added to but the cube will not register the added waypoints and instead gets stuck in a point in space which is unrelated to any of the instantiated waypoints.

I'm sure it's something very simple which I have overlooked. I have tried searching for similar problems but without much luck.

The code:

 #pragma strict
 
 import System.Collections.Generic;
 
 //var waypointList = new List.< Transform>();
 var waypoint : Transform[];
 var speed : float = 20;
 var currentWaypoint : int = 0;
 
 var insWP : GameObject;
 var wpCookie : GameObject;
 var ray : Ray;
 var hit : RaycastHit;
 var hoverWP : Vector3;
 
 var loop : boolean = true;
 
 
 function Update(){
 
 
 if (Input.GetButtonDown ("Fire1")) {
             // Construct a ray from the current mouse coordinates
             var ray : Ray = Camera.main.ScreenPointToRay (Input.mousePosition);
             
             if (Physics.Raycast (ray, hit)) 
                 {
                 
                 hoverWP = Vector3(hit.point.x, hit.point.y + 10, hit.point.z); 
             
                 Instantiate (insWP, hoverWP, transform.rotation);
                 Instantiate (wpCookie, hit.point, Quaternion.identity);
                 
                 
                 addToArray( insWP );
                 Debug.Log(waypoint.length);
                 
                 }
 }
 
     
     if(currentWaypoint < waypoint.length)
     {
 
     //var target : Vector3 = waypoint[currentWaypoint].position;
     
     var moveDirection : Vector3 = waypoint[currentWaypoint].transform.position - transform.position;
 
     var velocity = rigidbody.velocity;
 
         if(moveDirection.magnitude < 1)
         {
         currentWaypoint++;
         }
         
         else
         {
         velocity = moveDirection.normalized * speed;
         }
     
         
     rigidbody.velocity = velocity;
     
     
 
     }
     
     else
     {
         if(loop)
         { 
         currentWaypoint = 0;
         }
         else
         {
         velocity = Vector3.zero;
         }
     }
 
 }
 
 
 function addToArray ( obj : GameObject)
 
 {
  
     waypoint += [obj.transform];
  
 }