Yeah, it's surprising, some of it is so wrong.
Realistically the game needs remaking from the ground up.
Update :
I just spent the best part of a day writing a plugin for Blender to help speed up the process of realigning the misaligned vertices throughout Manaan.
The script also works for Objects in Blender, because why not.
I kept looking at the "Snap -> Selection to Active" button in the menu, thinking it could help if only it did a single axes, but there wasn't an option for only using one, so I made it happen.
Edit : More Manaan fixes.