How do I globally (per project) replace/edit the builtin Standard PBR (Metallic/Specular) shaders with custom ones?

as far as I can tell, you can't update the builtin Standard shader, but you CAN update the builtin CGincludes in C:\Program Files\wherever your editor install is\Editor\Data\CGIncludes (that isn't per-project though, it's everything on that editor version.) If your shaders use the same properties as the standard shader, you could update the CGincludes referenced by the Standard shader (eg, "UnityStandardCoreForward.cginc" to do your thing instead, but tbh I can't recommend doing something like this so close to shipping because it would probably initially break the hell out of all your other surface shaders (and possibly some of your frag shaders too!)

As far as mass-changing shaders on materials, here's my route (simplified for space and readability). I have an Editor Utilities class where I keep editor API helper methods, and in that class I put

 public static List<Material> GetMaterials()
     {
         var matFiles = GetFiles(GetSelectedPathOrFallback()).Where(s => s.Contains(".mat"));
 
         List<Material> toReturn = new List<Material>();
         foreach (string str in matFiles)
         {
             Material mat = (Material)AssetDatabase.LoadAssetAtPath(str, typeof(Material));
             if (mat != null && !toReturn.Contains(mat)) toReturn.Add(mat);
         }
         return toReturn;
     }

which returns a list of all materials in the currently selected directory in Assets. (if none is selected, it'll run the search of ALL your assets.)

this uses a great utility method that I didn't write,

 //https://gist.github.com/kimsama/ff69cca140468f92d755
 public static string GetSelectedPathOrFallback()
 {
     string path = "Assets";
 
     foreach (UnityObject obj in Selection.GetFiltered(typeof(UnityObject), SelectionMode.Assets))
     {
         path = AssetDatabase.GetAssetPath(obj);
         if (!string.IsNullOrEmpty(path) && File.Exists(path))
         {
             path = Path.GetDirectoryName(path);
             break;
         }
     }
     return path;
 }

Then have an editor window that creates a dictionary of the shaders you want to replace and the shaders you want to replace them with and use that to replace all the materials in the current directory. to avoid having half the answer be taken up by EditorGUI code, I'll show a hardcoded dictionary, but ideally you'd actually get the shaders from object fields.

 using UnityEngine;
 using UnityEditor;
 using System.Collections.Generic;
 using System;
 using System.Linq;
 public class ShaderStandardizer : EditorWindow
 {
 private Dictionary<Shader, Shader> toReplace = new Dictionary<Shader, Shader>();
         private bool initialized;
         [MenuItem("Tools/MyTools/Shader Replacer")]
         private static void OpenWindow()
         {
             GetWindow<ShaderStandardizer>().Show();
         }
         void InitializeDictionary()
         {
             if (!initialized)
             {
                 toReplace.Add(Shader.Find("Standard"), Shader.Find("MyStudio/Category/ShaderName"));
                 toReplace.Add(Shader.Find("Standard (Specular setup)"), Shader.Find("MyStudio/Category/OtherShaderName"));
                 toReplace.Add(Shader.Find("Legacy Shaders/Bumped Specular"), Shader.Find("MyStudio/OtherCategory/ShaderName"));
                 initialized = true;
             }
         }
         protected override void OnGUI()
         {
             InitializeDictionary();
             if (GUILayout.Button("Replace"))
             {
                 string path = MyEditorUtils.GetSelectedPathOrFallback();
                 if (path != "Assets" || EditorUtility.DisplayDialog(
                     "Search from root?",
                     "Searching all assets from root can potentially lock Unity. Proceed?",
                     "OK", "Cancel"))
                 {
                     List<Material> materials = MyEditorUtils.GetMaterials().FindAll(m => toReplace.Keys.Contains(m.shader));
                     string title = string.Format("Update {0} materials?", materials.Count);
                     string message = string.Format("This operation will update {0} materials in {1} and subfolders. Proceed?", materials.Count, path);
                     string report = "UPDATED";
                     if (EditorUtility.DisplayDialog(title, message, "OK", "Cancel"))
                     {
                         foreach (Material material in materials)
                         {
                             report += string.Format("\n{0} from {1} to {2}", AssetDatabase.GetAssetPath(material), material.shader.name, materials[material.shader].name);
                             material.shader = materials[material.shader];
                         }
                     }
                     //use System.IO to write the report to a text file or something
                 }
             }
         }
         protected void OnDisable()
         {
             Resources.UnloadUnusedAssets();
         }
 }