Trying to setup a good crouching mechanism

So right now everything works great, except that every once in a while the player teleports to 0 on the y axis. It's because I'm setting the position of the player. That's the problem, but I don't know how to fix it without messing up my crouching mechanic. Here's my code:

Code (csharp):

1.  
2. using UnityEngine;
3. using System.Collections;
4.  
5. public class PlayerMovement : MonoBehaviour
6. {
7.    
8.     //Public Variables
9.         //Movement Variables
10.     public float moveSpeed = 3.0f;
11.     public float sprintSpeed = 6.0f;
12.     public float crouchSpeed = 1.5f;
13.     public float crouchHeight = 1.0f;
14.     public float crouchTransitionSpeed = 5.0f;
15.     public float crouchingJumpPower = 0.0f;
16.     public float jumpPower = 7.5f;
17.     public float wallJumpPushOffPower = 3.0f;
18.     public float wallJumpPushUpPower = 7.5f;
19.     public float minWallCollisionAngle = 60.0f;
20.     public float gravity = -20.0f;
21.         //Input Variabes
22.     public string moveAxisX = "Horizontal";
23.     public string moveAxisZ = "Vertical";
24.     public string sprintButton = "Sprint";
25.     public string crouchButton = "Crouch";
26.     public string jumpButton = "Jump";
27.     //Hidden Variabes
28.    
29.     //Private Variables
30.         //Movement Variables
31.     private Vector3 movement;
32.     private bool crouching;
33.         //Component Variables
34.     private CharacterController controller;
35.  
36.     void Start ()
37.     {
38.         //We have to tell the controller variable what CharacterController we want to be changing.
39.         //In this case it's the CharacterController on the object that this script is attached to.
40.         controller = this.GetComponent<CharacterController>();
41.     }
42.     void Update ()
43.     {
44.         //We are calling the PlayerMovement method; it holds all the movement functionality for organization.
45.         Movement ();
46.     }
47.     void OnControllerColliderHit (ControllerColliderHit collision)
48.     {
49.         if(!controller.isGrounded)
50.         {
51.             if(Vector3.Angle(this.transform.forward, collision.normal) > minWallCollisionAngle)
52.                 if(Input.GetButtonDown(jumpButton))
53.                     WallJump(collision.normal);
54.         }
55.     }
56.     void Movement ()
57.     {
58.         //If the player is touching the ground he will be able to move and jump
59.         if(controller.isGrounded)
60.         {
61.             movement = new Vector3(Input.GetAxis(moveAxisX), 0, Input.GetAxis(moveAxisZ));
62.             //We have to turn the movement vector into world space instead of local.
63.             movement = transform.TransformDirection(movement);
64.             //If the player is holding down the sprint button we'll multiply movement by sprintSpeed.
65.             if(Input.GetButton(sprintButton))
66.             {
67.                 movement *= sprintSpeed;
68.                 crouching = false;
69.             }
70.             //If the player isn't holding the sprint button but IS holding the crouch button we'll multiply movement by crouchSpeed.
71.             else if(Input.GetButton (crouchButton))
72.             {
73.                 movement *= crouchSpeed;
74.                 controller.height = Mathf.Lerp(controller.height, crouchHeight, crouchTransitionSpeed * Time.deltaTime);
75.                 this.transform.position = new Vector3(this.transform.position.x, controller.height / 2, this.transform.position.z);
76.                 crouching = true;
77.             }
78.             //Otherwise we'll multiply movement by moveSpeed because the player isn't sprinting.
79.             else
80.             {
81.                 movement *= moveSpeed;
82.                 controller.height = Mathf.Lerp(controller.height, 2, crouchTransitionSpeed * Time.deltaTime);
83.                 this.transform.position = new Vector3(this.transform.position.x, controller.height / 2, this.transform.position.z);
84.                 crouching = false;
85.             }
86.             //If the player presses the jump button we'll set the players y movement to the value of jumpPower.
87.             if(Input.GetButtonDown(jumpButton))
88.             {
89.                 if(!crouching)
90.                     movement.y = jumpPower;
91.                 else if(crouching)
92.                     movement.y = crouchingJumpPower;
93.             }
94.         }
95.         //Whether or not the player is touching the ground we'll still move the player down at the speed of the gravity variable.
96.         movement.y += gravity * Time.deltaTime;
97.         //By this point the movement variable is calculated correctly and we can now move the player in its direction.
98.         controller.Move(movement * Time.deltaTime);
99.     }
100.     void WallJump (Vector3 normal)
101.     {
102.         movement = Vector3.Reflect(transform.forward, normal);
103.         movement *= wallJumpPushOffPower;
104.         movement.y = wallJumpPushUpPower;
105.     }
106. }