I had the exact same problem with Noggit, I was getting frustrated not finding a solution so I checked perhaps if my WoWModding Folder (That I had downloaded from Noggit Beginner Guide) which holds also my WoW Files in a subfolder and it was write protected, thats the reason why Noggit couldn´t access the files, named in the log file.
So to change that:

1. Go to your "Master" folder, it holds the rest of your modding stuff including WoW Directory (Or just the WoW Directory, depends on you   )
2. Right click the "Master" folder
3. Click Properties
4. Uncheck the Write Protection
5. Click apply


Now it should work, well it worked for me