eeeehhhCan u again describe what exactly is the problem ? Sorry but i dont see what up ...
You have to check motx structure and find missing .blp file. The best way would be to copy hex code of structure and then add it into the .txt file. That .txt would be your file list for WoD extractor. Just extract them all and put into your patch.
if you converted them with 010 editor,im sure you deleted some wrong offsets ( 0x8 / 0x10 or something like that)
It's hard to see what you're working with, you're zoomed in too far, fly out a bit and show your character so atleast we can see what's going on from a wider perspective. Like my cataclysm shot here:
Did you ever think that maybe the invisible areas where normally they have stuff there may not actually be part of the WMO? It could possibly be part of the ADT/Map. As ADT files can have doodads and objects spawned around as well.
Try looking into how it looks in Machinima Studio without any editing to it. See if it has those parts shown properly. Also, do these invisible areas have collision?