Assigning Waypoints to an instantiated enemy

Hi,

I have a 'Boss' that instantiates itself when all enemies are defeated. Here is the JS (attached to each enemy):

 public static var enemyCount : int = 3;
  
 function OnCollisionEnter( collision : Collision ) 
  {
       if(collision.gameObject.tag == "fireball")
       {
       animation.Play("dying");
       audio.Play();
  yield WaitForSeconds(0.2);
          GameObject.Destroy ( gameObject ) ;
          enemyCount -= 1;
 }
 if(enemyCount <= 0) {
 var instance : GameObject = Instantiate(Resources.Load("boss"));
   }
 }

I also have a C# script that deals with enemies patrolling Waypoints and chasing the player if they wander within a certain distance from the player. This script is also attached to the enemies, as well as the boss himself. However, I cannot assign Waypoints to the boss like I can to the other enemies. From researching I've read you cannot do this to instantiated objects.

Is there any way around this? Your help would be much appreciated. Many thanks!

EDIT: C# script for Waypoint finding and player chasing/attacking:

 using UnityEngine;
 using System.Collections;
 
 public class EnemyMovementController : MonoBehaviour 
 {
     // speed of the AI player
     public int speed = 4;
     
     // speed the ai player rotates by
     public int rotationSpeed = 5;
     
     // the waypoints
     public Transform[] waypoints;
     
     // current waypoint id
     private int waypointId = 0;
     
     // the character controller component
     private CharacterController characterController;
 
     private Transform player;
 
     public int chasingDistance = 30;
 
     private bool attacking = false;
 
     /**
         Init
     */
     void Start()
     {
                 // retrieve this GameObjects CharacterController Component and store in characterController (todo)
         characterController = gameObject.GetComponent<CharacterController>();
         player = Motor.Instance.transform;
     }
     
     /**
         Patrol around the         waypoints
     */
     void Patrol()
     {
         // if no waypoints have been assigned
         if (waypoints.Length == 0) 
         {
             //Debug.LogError("You need to assign some waypoints within the Inspector!");
             return;
         }
         
         // if distance to waypoint is less than 2 metres then start heading toward next waypoint
         if (Vector3.Distance(waypoints[waypointId].position, transform.position) < 2)
         {
             // increase waypoint id
             waypointId++;
             
             // make sure new waypointId isn't greater than number of waypoints
             // if it is then set waypointId to 0 to head towards first waypoint again
             if (waypointId >= waypoints.Length) waypointId = 0;
         }
         
         // move towards the current waypointId's position
         MoveTowards(waypoints[waypointId].position);
         attacking = false;
     }
     
     /**
         Update - Every Frame
     */
     void Update()
     {
 
         PatrolAndChase ();
         }
             
     
     /**
         Move towards the targetPosition
     */
     void MoveTowards(Vector3 targetPosition)
     {
         // calculate the direction to waypoint
         Vector3 direction = targetPosition - transform.position;
         
         // rotate over time to face the target rotation - Quaternion.LookRotation(direction)
         transform.rotation = Quaternion.Slerp (transform.rotation, Quaternion.LookRotation(direction), rotationSpeed * Time.deltaTime);
         
         // set the x and z axis of rotation to 0 so the agent stands upright (otherwise equals REALLY bad leaning)
         transform.eulerAngles = new Vector3(0, transform.eulerAngles.y, 0);
         
         // use the CharacterController Component's SimpleMove(...) function
         // multiply the agent's forward vector by the speed to move the AI
         characterController.SimpleMove(transform.forward * speed);
         
         // crossfade the walking animation (todo)
         animation.CrossFade("walking",0.2F);
         
     }
     void PatrolAndChase()
     {
                 // calculate the distance to the player
                 int distanceToPlayer = (int)Vector3.Distance (player.transform.position, transform.position);
         
                 // calculate vector direction to the player
                 Vector3 directionToPlayer = transform.position - player.transform.position;
         
                 // calculate the angle between AI forward vector and direction toward player
                 // we use Mathf.Abs to store the absolute value (i.e. always positive)
                 int angle = (int)Mathf.Abs (Vector3.Angle (transform.forward, directionToPlayer));
         
                 // if player is within 30m and angle is greater than 130 then begin chasing the player
                 if (distanceToPlayer < chasingDistance && angle > 130) {
                         // move towards the players position
                         //MoveTowards (player.transform.position);
             
                         // attack the player ONLY if not already attacking
                         if (!attacking && distanceToPlayer < 4) {
                                 StartCoroutine (Attack ());
                         } else if (!attacking) {
                                 // player is "out of sight"
                                 MoveTowards (player.transform.position);
                         }
                 } else {
                         // patrol
                         Patrol ();
             
                         // if attacking, then toggle to stop
             
                 }
 
         }
 
         /**
     Fire at the player
 */
     IEnumerator Attack()
     {
         // toggle attacking on
         attacking = true;
         
         // crossfade the attacking animation
         animation.CrossFade("jump", 0.2F);
         
         // odds of player being attacked successfully
         float odds = Random.Range(0.0f, 1.0f);
         
         // was the player attacked?
         if (odds >= 0.0f)
         {
             // player has been attacked
             HealthController.Instance.HasBeenAttacked();
         }
         
         // create delay before attacking again (else would be constant every frame = dead player)
         yield return new WaitForSeconds(1);
 
         
         // allow attacking again
         attacking = false;
     }
 }