Saving layout and enemy stats with Binary Formatter

So I'm using a binary formatter to save the variables of my script as well as I can. When it comes to the player, everything works perfectly. However I also have an interchanging map aswell as a list of enemies that need to be added aswell. For example, you right click something to activate an animation and delete its collision box. The problem I'm having is, I really need to undo the animation and reset the collision box through a saving and loading system. It's not much of a reverse time rather then a reset to its original variables, including enemy health and location. I would like to be able to list a few enemies, there health, location, and everything else that needs changing, but in order to do that I would need to keep track of the scripts and where they are, but its impossible to save a script prefab, IE:

 [System.Serializable]
 public class EnemyVariables
 {
     public enemyEssentials ESScript;
     public float enemyHealth;
     public float locationX;
     public float locationY;
     public bool isAlive;
 }

will not work. What I currently have is all of that before without actually saving it to my data. IE:

     public void Save ()
     {
         Debug.Log ("Save was started");
         BinaryFormatter bf = new BinaryFormatter ();
         FileStream file = File.Create (Application.persistentDataPath + "/playerInfo.dat");
 
         PlayerData data = new PlayerData ();
 
         //SAVE DATA HERE//
         data.CharacterLocationX = CharacterLocation.x;
         data.CharacterLocationY = CharacterLocation.y;
         data.Health = Health;
         data.Experience = Experience;
         data.Level = Level;
         data.damageLevel = damageLevel;
         data.healthLevel = healthLevel;
         data.delayLevel = delayLevel;
         data.dodgeLevel = dodgeLevel;
         data.ugradeTokens = ugradeTokens;
         data.CUGTokens = CUGTokens;
         data.SpendableCUGTokens = SpendableCUGTokens;
         data.CUGM = CUGM;
         data.tutorialTaskVariables = tutorialTaskVariables;
 
         for (int z = 0; z < enemyVariables.Count; z++) {
             if (enemyVariables [z].ESScript != null) {
                 enemyVariables [z].locationX = enemyVariables [z].ESScript.transform.position.x;
                 enemyVariables [z].locationY = enemyVariables [z].ESScript.transform.position.y;
                 enemyVariables [z].enemyHealth = enemyVariables [z].ESScript.Health;
                 enemyVariables [z].isAlive = enemyVariables [z].ESScript.gameObject.activeSelf;
             }
         }
 
         bf.Serialize (file, data);
         file.Close ();
     }

as you should be able to tell, enemyVariables is not being saved into the saving function otherwise it would work, but it will save temporarily until you exit and re-enter the game. I was curious if there was a work around without having to use exact gameobjects, transforms or scripts so I can get this working. I also would like to know if there is a way to save the map layout for re-enters because I don't currently have that. Of course I could consider it a "Feature" to re-load the specific stats and not the map layout itself but getting things as polished as I can would be even more beautiful...

Thank you so much in advance! - Seth Albertus