Replace an object in a prefab with another prefab?

Ok here is what I want to do. I have a Maya model which is a room with several cubes in it. Then I have a library (folder) of complex models (also Maya). I am using PostProcessForMaya : AssetPostprocessor to do things like find all cubes with the name PointLight and delete their mesh, colliders, and renderer then attach a light component and set its attributes. Now when I drag that into my project I have lights. So far all of that is working. And I am trying to avoid creating a prefab in another folder with all the added or changed things. I don't like the idea of duplicate data.

But the second thing I wanted to do was find all cubes named "Desk" and replace them with detailed desk models. The problem is that I cannot just make the cube's transform equal the desk transform because the desk is made up of several smaller parts. SO this is not working. All I want is to take a cube and replace it with a desk. I have already figured out how to create an empty GO, Instantiate the Office model, replace cubes with desks, and save it back as a prefab to my library. But again, that is now duplicate data. I plan on these files getting very large, on the verge of crashing Unity (where is x64 editor? lol), so having duplicates is a bad idea.

Also, I am aware that there are packages on the asset store that do this sort of thing. But I will need very granular control over this script for other reasons. Also working for a corporation means I cant just go pick up a package without signing a lot of internal paperwork, doing a security assessment, getting an IT concur/ review, talking to lawyers about licenses, and finally getting purchasing involved to maintain the license. So purchasing a package from the Unity store that does this sort of thing is out of scope of my project.

Anyways, here is the code. It is a little messy but that is because it is still very much a work in progress. Any help would be appreciated.

Code (csharp):

1.  
2. //-------------------------------------------//
3. //
4. // Place this in a folder named "Editor"
5. //
6. //-------------------------------------------//
7.  
8. using UnityEngine;
9. using UnityEditor;
10. using System.Collections;
11. using System.Text.RegularExpressions;
12. using System.IO;
13. using System;
14.  
15. public class PostProcessForMaya : AssetPostprocessor
16. {
17.     private string flStructures = "/[ModEls]/StruCturEs/"; //Not case sensitive, we convert everything ToLower later
18.  
19.     //strings for naming conventions. Mostly here so I can use .ToLower() on them
20.     private string sLight = "Light";
21.     private string sDeskPlaceHolder = "DeskPlaceHolder";
22.  
23.     private void OnPostprocessModel(GameObject g)
24.     {
25.         string lowerCaseAssetPath = assetPath.ToLower();
26.         if (lowerCaseAssetPath.IndexOf(flStructures.ToLower()) == -1)
27.             return; //If it is not in the structures folder we wont post-process it
28.  
29.         //Do something to each file found in the folder
30.         Apply(g.transform);
31.         //Lets make sure the devs know something just happened
32.         Debug.Log(g.name + " has just been post-processed on " + DateTime.Now.ToString("dddd, dd-MMM-yyyy") + " at " + DateTime.Now.ToString("hh:mm tt"));
33.     }
34.  
35.     private void Apply(Transform transform)
36.     {
37.         //Make everything static for lightmapping
38.         transform.gameObject.isStatic = true;
39.        
40.         //Look for lights...
41.         if (transform.name.ToLower().Contains(sLight.ToLower()))
42.             LightRules(transform);
43.  
44.         //Replace Desks
45.         if (transform.name.ToLower().Contains(sDeskPlaceHolder.ToLower()))
46.             DeskRules(transform.gameObject);
47.  
48.         foreach (Transform child in transform)
49.             Apply(child); //cycle through all children of the current transform
50.     }
51.  
52.     private void LightRules(Transform transform)
53.     {
54.         //Remove colliders. Not needed for lights.
55.         //Had to use UnityEngine.Object because we are also using "using.System" which has an Object reference
56.         Component[] mr = transform.gameObject.GetComponentsInChildren(typeof(MeshRenderer), true);
57.         foreach (MeshRenderer o in mr) { UnityEngine.Object.DestroyImmediate(o, true); }
58.         Component[] mf = transform.gameObject.GetComponentsInChildren(typeof(MeshFilter), true);
59.         foreach (MeshFilter o in mf) { UnityEngine.Object.DestroyImmediate(o, true); }
60.         Component[] mc = transform.gameObject.GetComponentsInChildren(typeof(MeshCollider), true);
61.         foreach (MeshCollider o in mc) { UnityEngine.Object.DestroyImmediate(o, true); }
62.  
63.         //If it has a renderer then make it a light
64.         transform.gameObject.AddComponent(typeof(Light));
65.         //Set the light properties
66.         transform.light.type = LightType.Point;
67.         transform.light.shadows = LightShadows.Soft;
68.         transform.light.shadowBias = 0.002f;
69.         transform.light.intensity = 0.25f;
70.         transform.light.range = 6.0f;
71.     }
72.  
73.     private void DeskRules(GameObject g)
74.     {
75.         // create an empty gameobject and add the mesh as a child
76.         UnityEngine.Object prefab = (UnityEngine.Object)Resources.Load("Library/Desk_L_Small");
77.         //GameObject newGO = Instantiate (gameObject, Vector3.zero, Quaternion.Identity);
78.         //transform = prefabRoot.transform;
79.  
80.         //UnityEngine.Object newObject;
81.         //newObject = (GameObject)Resources.Load("Library/Desk_L_Small");
82.  
83.         // create the prefab, and connect the dummy prefab root to it
84.         PrefabUtility.ReplacePrefab(g, prefab, ReplacePrefabOptions.ReplaceNameBased);
85.         //EditorUtility.ReplacePrefab(prefabRoot, prefab, ReplacePrefabOptions.ConnectToPrefab);
86.  
87.         Debug.Log("Processing Desk");
88.         //GameObject newObject;
89.         //PrefabUtility.InstantiatePrefab(newObject);
90.         //GameObject.Instantiate(newObject,transform.position,transform.rotation);
91.         //newObject.transform.position = transform.position;
92.         //newObject.transform.rotation= transform.rotation;
93.         //newObject.transform.parent = transform.parent;
94.         //newObject.transform.name = transform.name;
95.  
96.         //cleanup the gameobject instance in the scene
97.         //UnityEngine.Object.DestroyImmediate(prefabRoot);
98.     }
99. }
100.