Unity mistaking one object for another

It's hard to describe my problem without actually uploading my game file but I'll try. Basically I have a script that works PERFECTLY when I pick up a sword and an axe and vice versa and whatever. However, when I try copy and pasting either one and picking it up in game, Unity thinks that it's the object I copy and pasted from. So if I try picking up the original sword everything's fine, however if I pick up the copy (same name and everything, all variables are assigned properly) it sets the original to Vector3.zero in stead of the copy but still parents the copy correctly, just nothing else works.

 var crosshair : GUITexture;
 var player : GameObject;
 var layermask : LayerMask;
 var halo : GameObject;
 var weapon_id : float;
 var shield_id : float;
 var torch : GameObject;
 var right_arm_weapon : GameObject;
 var left_arm_weapon : GameObject;
 private var isShield : boolean;
 
 function Start () {
 
 if (weapon_id > 0){
 
 isShield = false;
 }
 else
 {
 isShield = true;
 }
 
 
 }
 function Update () {
     var ray : Ray = Camera.main.ViewportPointToRay(crosshair.transform.position);
 
     var hit : RaycastHit;
 
     
     if(Physics.Raycast(ray, hit, Mathf.Infinity, layermask))
        {
               if (hit.transform.name == gameObject.transform.name && Vector3.Distance(transform.position, player.transform.position) <= 3)
               {
                   halo.GetComponent("Halo").enabled = true;
                   if (Input.GetKeyDown(KeyCode.E))
                 {
                     if (isShield == false){
                     //Drop Current Weapon
                         if(player.GetComponent("PlayerScript").weapon_id != 0){
                             player.GetComponent("PlayerScript").currentWeapon.transform.localScale = Vector3(1,1,1);
                             player.GetComponent("PlayerScript").currentWeapon.gameObject.layer = LayerMask.NameToLayer("Default");
                             player.GetComponent("PlayerScript").currentWeapon.gameObject.AddComponent("Rigidbody");
                             player.GetComponent("PlayerScript").currentWeapon.collider.isTrigger = false;
                             right_arm_weapon.transform.DetachChildren();
                         }
                     //Equip New Weapon
                       player.GetComponent("PlayerScript").weapon_id = weapon_id;
                       player.GetComponent("PlayerScript").currentWeapon = hit.transform.gameObject;
                       gameObject.transform.parent = right_arm_weapon.transform;
                       player.GetComponent("PlayerScript").SwitchWeapon();
                       }
                       else
                       {
                       //Drop Current Shield
                           if(player.GetComponent("PlayerScript").shield_id != 0){ //if the player has a shield
                             player.GetComponent("PlayerScript").currentShield.transform.localScale = Vector3(1,1,1); //returns shield to regular size
                             player.GetComponent("PlayerScript").currentShield.gameObject.layer = LayerMask.NameToLayer("Default"); //sets layer to default
                             player.GetComponent("PlayerScript").currentShield.gameObject.AddComponent("Rigidbody"); //adds the rigidbody
                             player.GetComponent("PlayerScript").currentShield.collider.isTrigger = false; //lets it collide with the world again
                             left_arm_weapon.transform.DetachChildren(); //detachs it from player
                         }
                       //Equip New Shield
                       player.GetComponent("PlayerScript").shield_id = shield_id; //sets shield id in other script
                       player.GetComponent("PlayerScript").currentShield = hit.transform.gameObject; //sets gameObject variable to what the player picked up
                       gameObject.transform.parent = player.GetComponent("PlayerScript").left_arm_weapon.transform; //parents this new shield to left_arm
                       player.GetComponent("PlayerScript").SwitchShield(); //calls function to switch shield
                       }
                       halo.particleSystem.enableEmission = false;
                 }
 
             }
         else
             {
                 halo.GetComponent("Halo").enabled = false;
             }
 
     }
     
 }

The shield part is the same as the weapon part, works fine but still has the problem with the copying thing.

(This is the switch weapon function in my other script)

 function SwitchWeapon () {
     if (weapon_id == 0){
         right_arm.renderer.enabled = false;
         currentWeapon.renderer.enabled = false;
     }
     
     if (weapon_id == 1){
         right_arm.renderer.enabled = true;
         right_arm.animation.Play("left_arm_up");
         currentWeapon.collider.isTrigger = true;
         currentWeapon.transform.localPosition = Vector3(0, 0, 0);
         currentWeapon.transform.localRotation = Quaternion.Euler(270,0,0);
         Destroy(currentWeapon.rigidbody);
         currentWeapon.gameObject.layer = LayerMask.NameToLayer("Weapon");
     }
     
     if (weapon_id == 2){
         right_arm.renderer.enabled = true;
         right_arm.animation.Play("left_arm_up");
         currentWeapon.collider.isTrigger = true;
         currentWeapon.transform.localScale = Vector3(1.3,1.1,1.5);
         currentWeapon.transform.localPosition = Vector3(0, 0, 0);
         currentWeapon.transform.localRotation = Quaternion.Euler(270,346.2527,0);
         Destroy(currentWeapon.rigidbody);
         currentWeapon.gameObject.layer = LayerMask.NameToLayer("Weapon");
     }
     
     
 
 }

Everything worked perfectly except for when I try to copy it. I even have a halo set up on the objects so when I hover over them with my cursor they light up to indicate that you're looking at it but when I copy it over and change the halo variable to the correct one, it still lights up both when you're only looking at the one. It doesn't make sense to me, can anyone help? Thanks