Problem with Jump script

Thanks everyone for participation again!

Here's working code

 public class New_Player_Controller : MonoBehaviour {
     public float speed = 6.0f;
     public float jumpSpeed = 8.0f;
     public float gravity = 20.0f;
     public float rotateSpeedGrounded = 3.0f; // Rotation speed at ground
 
     public float inAirSpeed = 2.0f; // Adds or substracts to the movementspeed in air
     public float inAirDrift = 0.5f; // Adds Sidewards drift in air
     public float inAirRotation = 0.5f; // Rotation speed in air. Uncomment this to let the player change the face direction in air
 
     public float extraJumpForce = 5.0f;         //How much extra force to give to our jump when the button is held down
     public float maxExtraJumpTime = 2.0f;       //Maximum amount of time the jump button can be held down for
     public float delayToExtraJumpForce = 2.0f;  //Delay in how long before the extra force is added
     private float jumpTimer;             //Used in calculating the extra jump delay
     private bool playerJumped = false;           //Tell us if the player has jumped
     private bool playerJumping = false;          //Tell us if the player is holding down the jump button
 
     private Vector3 moveDirection = Vector3.zero;
     private float inputModifyFactor = 1.0f;
     private bool isGrounded     = false;
     public Transform groundChecker;
     private bool pressedJump     = false;
     private bool unPressedJump     = false;
     public float maxJump = 10;
     private CharacterController controller = new CharacterController();
 
     void Start() {
 
         controller = GetComponent<CharacterController> ();
 
     }
 
     void Update() {
     
         if (!pressedJump) {
             pressedJump = Input.GetButtonDown ("Jump");
         }
 
         if (!unPressedJump) {
             unPressedJump = Input.GetButtonUp ("Jump");
         }
     }
 
     void FixedUpdate() { 
 
         isGrounded = Physics.Linecast (transform.position, groundChecker.position);
         //float rayDistance = controller.bounds.extents.y;
         //isGrounded = Physics.Raycast (transform.position, Vector3.down, rayDistance + 0.085f);
 
         //If our player hit the jump key, then it's true that we jumped!
         if (pressedJump) {
             if (isGrounded) {
                 
                 pressedJump = false;
                 playerJumped = true;   //Our player jumped!
                 playerJumping = true;  //Our player is jumping!
                 jumpTimer = Time.time; //Set the time at which we jumped
             }
         }
 
         //If our player lets go of the Jump button OR if our jump was held down to the maximum amount...
         if (unPressedJump || Time.time - jumpTimer > maxExtraJumpTime) {
             playerJumping = false; //... then set PlayerJumping to false
             unPressedJump = false;
         }
 
         //CharacterController controller = GetComponent<CharacterController> ();
         //            // ---------------------------------------- At Ground -----------------------------------------
         if (isGrounded) {
             moveDirection = new Vector3 (Input.GetAxis ("Horizontal"), 0, Input.GetAxis ("Vertical"));
             moveDirection *= speed;
             inputModifyFactor = (moveDirection.x != 0.0f && moveDirection.z != 0.0f) ? 0.7071f : 1.0f;
             moveDirection *= inputModifyFactor;
 
 
             if (playerJumped) {
                 moveDirection.y = jumpSpeed;
                 playerJumped = false;
             }
         }
         // ---------------------------------------------------- In Air  ----------------------------
         else {
             // We are not grounded. We can still influence the movement with the horizontal and vertical axis, but not so strong.
             moveDirection = new Vector3 (Input.GetAxis ("Horizontal"), moveDirection.y, Input.GetAxis ("Vertical"));
             moveDirection.x *= speed;
             moveDirection.z *= speed;
             moveDirection.y -= gravity * Time.deltaTime;
 
             if (moveDirection.y > maxJump) {
 
                 moveDirection.y = maxJump;
                 playerJumping = false;
 
             }
         }
         // ---------------------------------------------------------------------------------------------        
         //Rotate
         Vector3 curDir = new Vector3 (moveDirection.x, 0, moveDirection.z);
         Vector3 newDir = Vector3.RotateTowards (transform.forward, curDir, (isGrounded ? rotateSpeedGrounded : inAirRotation) * Time.deltaTime, 0.0F);
         Debug.DrawRay (transform.position, newDir * 10, Color.red);
         transform.rotation = Quaternion.LookRotation (newDir);
 
         //Move the controller
         if (moveDirection != Vector3.zero) {
             if (playerJumping && Time.time - jumpTimer > delayToExtraJumpForce){
                 moveDirection.y = moveDirection.y + extraJumpForce;
             }
 
             controller.Move (moveDirection * Time.deltaTime);
         }
 
     }
         
 }