What I had was actually a copy of everything, I had the complete copy of all files but also a bunch of duplicated .part files. The installer would try to use the .part files instead of the actual complete files. Not sure how this happened but I deleted all the incomplete stuff and cleaned up the directory. Once that was done it all worked and installed properly.
Files that should be in the directory
Diablo III Setup.app [folder]
Diablo III Setup
Installer Tome 1.MPQE
Installer Tome 2.MPQE
Installer Tome 3.MPQE
Thats it, if you have any other files or folders you can safely delete them. Just in case I am wrong you could move/copy them somewhere else first. However I'm certain this is all I needed to install the game.
I hope this helps someone, Good Luck!