The time scale being 0 doesn't have any effect on GUI buttons, so the problem must be elsewhere. Incidentally, for toggling things, you can use code like:

if (Input.GetKeyDown(KeyCode.P) ) {
    pauseVisible = !pauseVisible;
    Time.timeScale = 1.0-Time.timeScale;
    GetComponent(MouseLook).enabled = !GetComponent(MouseLook).enabled;
    cam.GetComponent(MouseLook).enabled = !cam.GetComponent(MouseLook).enabled;
    cam2.GetComponent(MouseLook).enabled = !cam2.GetComponent(MouseLook).enabled;
}

After scratching my head for ages finding nothing wrong i've discovered that I only reset Time.timeScale to 1.0 when pressing the 'P' key, but not when choosing an option in the menu. It wasn't until I commented out a yield statement that I discovered that the level was being loaded, but was not getting any further than my fade in script since time was at a stand still.

I've added lines to set Time.timeScale to 1.0 after pressing the buttons and it works perfectly now. My full, revised code is:

var click : AudioClip;
var menuSkin : GUISkin;
var areaWidth : float;
var areaHeight : float;
var theTexture : Texture2D;

static var pauseVisible : boolean;
private var player : GameObject;
private var cam : GameObject;
private var cam2 : GameObject;


function Start(){

    // initially hide the pause menu
    pauseVisible = false;
    player = GameObject.Find("First Person Controller");
    cam = GameObject.Find("Main Camera"); 
    cam2 = GameObject.Find("Secondary Camera"); 
}

function Update(){

    if( Input.GetKeyUp( KeyCode.P ) ){
        if(Time.timeScale == 1.0){
            Time.timeScale = 0;
            pauseVisible = true;
            player.GetComponent(MouseLook).enabled = false;
            cam.GetComponent(MouseLook).enabled = false;
            cam2.GetComponent(MouseLook).enabled = false;
        } else {

            Time.timeScale = 1.0;
            pauseVisible = false;
            player.GetComponent(MouseLook).enabled = true;
            cam.GetComponent(MouseLook).enabled = true;
            cam2.GetComponent(MouseLook).enabled = true;
        }
    }
}

function OnGUI () {

    if(pauseVisible){

        GUI.skin = menuSkin;

        GUI.color = Color.white;
        GUI.color.a = 0.5;
        GUI.DrawTexture(Rect(0, 0, Screen.width, Screen.height), theTexture);


        var ScreenX = ((Screen.width * 0.5) - (areaWidth * 0.5));
        var ScreenY = ((Screen.height * 0.5) - (areaHeight * 0.5));

        GUILayout.BeginArea(Rect(ScreenX, ScreenY, areaWidth, areaHeight));

        if(GUILayout.Button("Restart Level")){
            OpenLevel("level01");
            Time.timeScale = 1.0;
        }

        if(GUILayout.Button("Quit To Menu")){
            OpenLevel("menu");
            Time.timeScale = 1.0;
        }

        GUILayout.EndArea();
    }
}


function OpenLevel(level : String){
    audio.PlayOneShot(click);
    yield WaitForSeconds(0.35);
    Application.LoadLevel(level);

}

@script RequireComponent (AudioSource)

I need help with a slightly different code:

using UnityEngine;
using System.Collections;
using System.Collections.Generic;

public class MenuController : MonoBehaviour {

    static int difficulty = 1;
    public GUISkin skin;
    private List animationComponents;
    private List audioSourceComponents;
    private float menuOn = 0;
    private float lastTime = 0;

    int[] playerHitDamage = new int[5] {  3,  4,  6, 10, 20 };
    int[] playerHeal      = new int[5] {  5,  4,  3,  2,  0 };
    int[] enemyHitDamage  = new int[5] { 10,  5,  2,  2,  2 };
    int[] enemyHeal       = new int[5] {  0,  0,  0,  0,  0 };

    // Use this for initialization
    IEnumerator Start () {
        UpdateDifficulty();
        AudioListener.volume = 0;
        yield return 0;
        AudioListener.volume = 1;
    }

    // Update is called once per frame
    void Update () {
        // Don't pause in first frame - allow scripts to settle in first
        if (Time.timeSinceLevelLoad == 0)
            return;

        float realDeltaTime = (Time.realtimeSinceStartup - lastTime);
        lastTime = Time.realtimeSinceStartup;
        menuOn = Mathf.Clamp01(menuOn + (Time.timeScale == 0 ? 1 : -1) * realDeltaTime * 5);

        if (!Screen.lockCursor && Time.timeScale != 0) {
            StartCoroutine(Pause(true));
        }
    }

    void OnGUI () {
        if (menuOn == 0)
            return;

        GUI.skin = skin;

        // PLAY button
        Rect rect = new Rect(0, 0, 150, 75);
        rect.x = (Screen.width  - rect.width ) / 2 + (1 - menuOn) * Screen.width;
        rect.y = (Screen.height - rect.height) / 2;
        if (GUI.Button(rect, "PLAY")) {
            StartCoroutine(Pause(false));
        }

        // Difficulty buttons
        rect = new Rect(rect.x - 200, rect.y + 150, rect.width + 400, 40);
        string[] difficulties = new string[] {"NO FAIL", "EASY", "MEDIUM", "HARD", "INSANE"};
        int newDifficulty = GUI.SelectionGrid(rect, difficulty, difficulties, difficulties.Length);
        if (newDifficulty != difficulty) {
            difficulty = newDifficulty;
            UpdateDifficulty();
        }
    }

    IEnumerator Pause (bool pause) {
        // Pause/unpause time
        Time.timeScale = (pause ? 0 : 1);
        // Unlock/Lock cursor
        Screen.lockCursor = !pause;

        if (pause == true) {
            Object[] objects = FindObjectsOfType(typeof(Animation));
            animationComponents = new List();
            foreach (Object obj in objects) {
                Animation anim = (Animation)obj;
                if (anim != null && anim.enabled) {
                    animationComponents.Add(anim);
                    anim.enabled = false;
                }
            }
            objects = FindObjectsOfType(typeof(AudioSource));
            audioSourceComponents = new List();
            foreach (Object obj in objects) {
                AudioSource source = (AudioSource)obj;
                if (source != null && source.enabled /*&& source.isPlaying*/) {
                    audioSourceComponents.Add(source);
                    source.Pause();
                }
            }
        }
        else {
            // If unpausing, wait one frame before we enable animation component.
            // Procedural adjustments are one frame delayed because first frame
            // after being paused has deltaTime of 0.
            yield return 0;
            foreach (Animation anim in animationComponents)
                anim.enabled = true;
            foreach (AudioSource source in audioSourceComponents)
                source.Play();
            animationComponents = null;
        }
    }

    void UpdateDifficulty () {
        Object[] objects = FindObjectsOfType(typeof(HealthController));
        foreach (Object obj in objects) {
            HealthController health = (HealthController)obj;
            if (health.gameObject.tag == "Player") {
                health.healingSpeed = playerHeal[difficulty];
                health.hitDamage = playerHitDamage[difficulty];
            }
            else {
                health.healingSpeed = enemyHeal[difficulty];
                health.hitDamage = enemyHitDamage[difficulty];
            }
        }
    }
}

I didn't make this code and I want to get rid of it and use the code posted above.

I would be fine even if I could just get rid of the difficulty buttons and add a qiut to menu and a restart level button but for some reason, if I get rid of the code or even just the difficulty buttons, the game won't work properly.

Any help is appreciated

Thank you in advance (ps: this is for a 3rd person game and I only want one set difficulty witch is why I don't want the buttons.)