Player Instantiate rotaion problem

Hi, Im making a new 2.5D platformer game. When I spawn the player at the start of the game, He is rotated -90 Degrees on the Y axis but he still moves on the X axis. When I try to rotate him on spawn with this line of code:

 cam.SetTarget((Instantiate(player,Vector3.zero,Quaternion.Euler(0,90,0)as GameObject).transform)

He rotates but then he moves on the Z axis. So, I want to know how I can rotate him and still have him move on the X Axis.

Heres the Scripts (C#)

PlayerController.cs (Controls) using UnityEngine; using System.Collections;

 [RequireComponent(typeof(PlayerPhysics))]
 public class PlayerController : MonoBehaviour {
     
     // Player Handling
     public float gravity = 20;
     public float runSpeed = 50;
     public float acceleration = 30;
     public float jumpHeight = 12;
     
     private float currentSpeed;
     private float targetSpeed;
     private Vector2 amountToMove;
     
     private PlayerPhysics playerPhysics;
     private Animator animator;
     
     
     void Start () 
     {
         playerPhysics = GetComponent<PlayerPhysics>();
         animator = GetComponent<Animator>();
     }
     
     void Update () 
     {
         if (playerPhysics.movementStopped)
         {
             targetSpeed = 0;
             currentSpeed = 0;
         }
 
         animator.SetFloat("Speed", currentSpeed);
 
         //Input
         targetSpeed = Input.GetAxisRaw("Horizontal") * runSpeed;
         currentSpeed = IncrementTowards(currentSpeed, targetSpeed,acceleration);
     
         if (playerPhysics.grounded) 
         {
             amountToMove.y = 0;
             
             // Jump
             if (Input.GetButtonDown("Jump")) 
             {
                 amountToMove.y = jumpHeight;    
             }
         }
         
         amountToMove.x = currentSpeed;
         amountToMove.y -= gravity * Time.deltaTime;
         playerPhysics.Move(amountToMove * Time.deltaTime);
     }
     
     // Increase n towards target by speed
     private float IncrementTowards(float n, float target, float a) 
     {
         if (n == target) 
         {
             return n;    
         }
         else 
         {
             float dir = Mathf.Sign(target - n); // must n be increased or decreased to get closer to target
             n += a * Time.deltaTime * dir;
             return (dir == Mathf.Sign(target-n))? n: target; // if n has now passed target then 
                 //return target, otherwise return n
         }
     }
 }

PlayerPhysics.cs (Physics and RayCasting)

 using UnityEngine;
 using System.Collections;
 
 
 [RequireComponent (typeof(BoxCollider))]
 public class PlayerPhysics : MonoBehaviour {
     
     public LayerMask collisionMask;
     
     private BoxCollider collider;
     private Vector3 s;
     private Vector3 c;
 
     private Vector3 originalSize;
     private Vector3 originalCentre;
     private float colliderScale;
 
     private int collisionDivisionsX = 3;
     private int collisionDivisionsY = 10;
 
     private float skin = .005f;
     
     [HideInInspector]
     public bool grounded;
 
     [HideInInspector]
     public bool movementStopped;
     
     Ray ray;
     RaycastHit hit;
     
     void Start() 
     {
         collider = GetComponent<BoxCollider>();
         colliderScale = transform.localScale.x;
 
         originalSize = collider.size;
         originalCentre = collider.center;
         SetCollider(originalSize,originalCentre);
     }
     
     public void Move(Vector2 moveAmount) 
     {
         
         float deltaY = moveAmount.y;
         float deltaX = moveAmount.x;
         Vector2 p = transform.position;
         
         // Check collisions above and below
         grounded = false;
         
         for (int i = 0; i<collisionDivisionsX; i ++) 
         {
             float dir = Mathf.Sign(deltaY);
             float x = (p.x + c.x - s.x/2) + s.x/(collisionDivisionsX - 1) * i; // Left, centre and then rightmost point of collider
             float y = p.y + c.y + s.y/2 * dir; // Bottom of collider
             
             ray = new Ray(new Vector2(x,y), new Vector2(0,dir));
             Debug.DrawRay(ray.origin,ray.direction);
             Debug.DrawRay(ray.origin,ray.direction);
             if (Physics.Raycast(ray,out hit,Mathf.Abs(deltaY) + skin,collisionMask)) 
             {
                 // Get Distance between player and ground
                 float dst = Vector3.Distance (ray.origin, hit.point);
                 
                 // Stop player's downwards movement after coming within skin width of a collider
                 if (dst > skin) 
                 {
                     deltaY = dst * dir - skin * dir;
                 }
                 else 
                 {
                     deltaY = 0;
                 }
                 
                 grounded = true;
                 
                 break;
                 
             }
         }
 
         // Check collisions left and right
         movementStopped = false;
         for (int i = 0; i<collisionDivisionsY; i ++) 
         {
             float dir = Mathf.Sign(deltaX);
             float x = p.x + c.x + s.x/2 * dir;
             float y = p.y + c.y - s.y/2 + s.y/(collisionDivisionsY - 1) * i;
             
             ray = new Ray(new Vector2(x,y), new Vector2(dir,0));
             Debug.DrawRay(ray.origin,ray.direction);
             Debug.DrawRay(ray.origin,ray.direction);
             if (Physics.Raycast(ray,out hit,Mathf.Abs(deltaX) + skin,collisionMask)) 
             {
                 // Get Distance between player and ground
                 float dst = Vector3.Distance (ray.origin, hit.point);
                 
                 // Stop player's downwards movement after coming within skin width of a collider
                 if (dst > skin) 
                 {
                     deltaX = dst * dir - skin * dir;
                 }
                 else 
                 {
                     deltaX = 0;
                 }
 
                 movementStopped = true;
                 break;
                 
             }
         }
 
         if(!grounded && !movementStopped) 
         {
             Vector3 playerDir = new Vector3 (deltaX, deltaY);
             Vector3 o = new Vector3(p.x + c.x + s.x/2 * Mathf.Sign(deltaX),p.y + c.y + s.y/2 * Mathf.Sign(deltaY));
             Debug.DrawRay(o,playerDir.normalized);
             ray = new Ray(o,playerDir.normalized);
             
             if(Physics.Raycast (ray, Mathf.Sqrt (deltaX * deltaX + deltaY * deltaY), collisionMask))
             {
                 grounded = true;
                 deltaY = 0;
             }
         }
         
         Vector2 finalTransform = new Vector2(deltaX,deltaY);
         
         transform.Translate(finalTransform);
     }
 
     public void SetCollider(Vector3 size, Vector3 center)
     {
         collider.size = size;
         collider.center = center;
 
         s = size * colliderScale;
         c = center * colliderScale;
     }
 
     
 }
 

GameManager.cs (Spawning, Checkpoints & Misc) using UnityEngine; using System.Collections;

 public class GameManager : MonoBehaviour {
 
     public GameObject player;
     private GameCamera cam;
 
     // Use this for initialization
     void Start () 
     {
         cam = GetComponent<GameCamera>();
         //SpawnPlayer();
     }
     
     private void SpawnPlayer()
     {
         cam.SetTarget((Instantiate(player,Vector3.zero,Quaternion.Euler(0,90,0)as GameObject).transform);
     }
 
 }

GameCamera.cs (Camera Following) using UnityEngine; using System.Collections;

 public class GameManager : MonoBehaviour {
 
     public GameObject player;
     private GameCamera cam;
 
     // Use this for initialization
     void Start () 
     {
         cam = GetComponent<GameCamera>();
         //SpawnPlayer();
     }
     
     private void SpawnPlayer()
     {
         cam.SetTarget((Instantiate(player,Vector3.zero,Quaternion.Euler(0,90,0)as GameObject).transform);
     }
 
 }

Here are some Screenshots: