It's easiest to manage these sets if you download them to a seperate location than the main set.
After loading latest dat in CMP jump to the rebuilder and rebuild a set into an empty destination directory.
First rebuild attempt choose update pack as source path. Then execute another rebuild attempt and choose the main set as source path. After rebuild finishes you will be 100%
If you want help with all those files you listed then please attach a fixdat because I'm not gonna hunt those manually