How to instantiate prefabs with scripts attached?

I've a grid that spawns two different colour cubes onto it. Now I am trying to swap out the cubes for prefabs which I've attached scripts to but when the prefabs spawn the scripts are gone. I think I might be supposed to use Gameobjects for the prefabs but I'm not really sure what I'm doing.

EDIT: I know I can set the pink and yellow Cube to prefabs that are already in the scene and the scripts will work but I'd like to be able to instantiate prefabs that arent in the scene.

Any help would be much appreciated!

 using UnityEngine;
 using System.Collections;
 using System.Collections.Generic;
 
 public class MapGenerator : MonoBehaviour {
     
     public Transform tilePrefab;
     public Transform pinkCube;
     public Transform yellowCube;
     public Vector2 mapSize;
     public Vector2 zeroZero;
     
     [Range(0,1)]
     public float outlinePercent;
 
     List<Coord> allTileCoords;
     Queue<Coord> shuffledTileCoords;
 
     public int seed = 10;
     
     void Start() {
         GenerateMap ();
     }
     
     public void GenerateMap() {
         
         zeroZero = mapSize/2;
 
         allTileCoords = new List<Coord> ();
         for (int x = 0; x < mapSize.x; x ++) {
             for (int y = 0; y < mapSize.y; y ++) {
                 allTileCoords.Add(new Coord(x,y));
             }
         }
         shuffledTileCoords = new Queue<Coord> (Utility.ShuffleArray (allTileCoords.ToArray (), seed));
 
         string holderName = "Generated Map";
         if (transform.Find (holderName)) {
             DestroyImmediate (transform.Find (holderName).gameObject);
         }
         
         Transform mapHolder = new GameObject (holderName).transform;
         mapHolder.parent = transform;
         
         for (int x = 0; x < mapSize.x; x ++) {
             for (int y = 0; y < mapSize.y; y ++) {
                 Vector3 tilePosition = CoordToPosition(x,y);
                 Transform newTile = Instantiate (tilePrefab, tilePosition, Quaternion.Euler (Vector3.right * 90)) as Transform;
                 newTile.localScale = Vector3.one * (1 - outlinePercent);
                 newTile.parent = mapHolder;
             }
         }
 
         //Pinks
         int pinkCount = 1;
         for (int i =0; i < pinkCount; i ++) {
             Coord randomCoord = GetRandomCoord();
             Vector3 obstaclePosition = CoordToPosition(randomCoord.x,randomCoord.y);
             Transform newObstacle = Instantiate(pinkCube, obstaclePosition + Vector3.up * .5f, Quaternion.identity) as Transform;
             newObstacle.parent = mapHolder;
         }
         
         //Yellows
         int yellowCount = 5;
         for (int i =0; i < yellowCount; i ++) {
             Coord randomCoord = GetRandomCoord();
             Vector3 obstaclePosition = CoordToPosition(randomCoord.x,randomCoord.y);
             Transform newObstacle = Instantiate(yellowCube, obstaclePosition + Vector3.up * .5f, Quaternion.identity) as Transform;
             newObstacle.parent = mapHolder;
         }
         
         
         
     }
 
     Vector3 CoordToPosition(int x, int y) {
         return new Vector3 (-mapSize.x / 2 + 0.5f + x, 0, -mapSize.y / 2 + 0.5f + y);
     }
 
     public Coord GetRandomCoord() {
         Coord randomCoord = shuffledTileCoords.Dequeue ();
         shuffledTileCoords.Enqueue (randomCoord);
         return randomCoord;
     }
 
     public struct Coord {
         public int x;
         public int y;
 
         public Coord(int _x, int _y) {
             x = _x;
             y = _y;
         }
     }
 }