Jumping animation? Moving through objects? Syncing jump animation?

My player move back to the start position and slowly returns back to where he was as opposed to just moving up 1 slowly to simulate a jump. Also my jump animation and when he moves are not synced together how can i achieve this? Also I need to stop the player from going through objects like blocks and instead stop when he gets to them (Enless the player presses jump to jump onto it) Here is a video showing there problems. Link to Video

Here is my code(Im pretty sure the problem is in the last if statement):

 #pragma strict
 //Calling Variables
 var hit : RaycastHit;
 var ray : Ray;
 var direction : Vector3; 
 var moveSpeed : float;
 var rotateSpeed : float;
 var PlayerTransform : Transform;
 var targetPoint : Vector3;
 var targetRotation : Quaternion;
 var anim : Animator;
 var speed : float;
 var vara : float;
 var distance : Vector3;
 var isGrounded : boolean = false;
 var Jump : boolean;
 var positiona : float;
 var positionb : float;
 var positionc : float;
 var positiond : Vector3;
 
 function Start () {
 //Sets the correct numbers for speeds
 moveSpeed = 3;
 rotateSpeed = 50;
 PlayerTransform = transform;
 direction = PlayerTransform.position;
  anim = GetComponent(Animator);
  Jump = false;
 }
 
 function Update () {
 //Moves player twoords the raycast hitpoint
 PlayerTransform.position = Vector3.MoveTowards(PlayerTransform.position, targetPoint, moveSpeed * Time.deltaTime);
 //if the vector3 data of the raycast hitpoint and the players transform are = then stop the player from running or walking
 if(targetPoint == PlayerTransform.position){
 speed = 0;
 moveSpeed = 3;
 }
 Jump = false;
 anim.SetBool("Jump", Jump);
 //Send the speed of the player to the animator so it can update the animation
 anim.SetFloat("Speed", speed);
 //If the player clicks the mouse then send a ray out
 if(Input.GetMouseButton(0))
     {
     speed = 1;
     ray = Camera.main.ScreenPointToRay(Input.mousePosition);
     if(Physics.Raycast (ray, hit, 100))
     
     {
     
 
     direction = hit.point;
     
     targetPoint = hit.point;
     //Find the degree you need to rotate
     targetRotation = Quaternion.LookRotation(targetPoint - PlayerTransform.position);
     //Rotate the player to look at target
     transform.rotation = Quaternion.Slerp(PlayerTransform.rotation, targetRotation, rotateSpeed * Time.deltaTime);
     
     targetPoint.y = 0;
     //Send the speed of the player to the animator
     anim.SetFloat("Speed", speed);
     
     }
     
     }
 //If the shift key is being held down then make the player run
 if(Input.GetKey(KeyCode.LeftShift) && targetPoint != PlayerTransform.position)
 {
 speed = 2;
 moveSpeed = 5;
 anim.SetFloat("Speed", speed);
 }
 //If the shift key is not being held down then tell the player to walk if he is not at his destination yet
 else if(targetPoint != PlayerTransform.position){
 speed = 1;
 moveSpeed = 3;
 anim.SetFloat("Speed", speed);
 }
 if (Input.GetKey(KeyCode.Space))
 {
 Jump = true;
 anim.SetBool("Jump", Jump);
 
 positiona = 1;
 PlayerTransform.position.x = positionb;
 PlayerTransform.position.z = positionc;
 positiond = Vector3(positionb, positiona, positionc);
 PlayerTransform.position = Vector3.Lerp(PlayerTransform.position, positiond, Time.deltaTime / 100); 
 }
 }