I've been away for awhile and just saw these posts. Sorry you guys are having trouble.
I just downloaded the mod from the link and installed it according to the instructions in the Readme and everything worked fine. I suspect the problem is that you didn't rename the mod folder by removing the "2D" or "3D" prefix.
As explained in the Readme, the download contains two versions -- the original "2D" version with 2D Leaderheads and a new "3D" version with 3D Leaderheads for Davis and Lee. Unzip and rename the version of your choice by removing the "2D" or "3D" prefix. In other words, the folder you put in your BTS/Mods folder should be named "Confederate States of America" -- with the "2D" or "3D" prefix removed.
If you look inside your mod folder now, I suspect you'll find two Config files. If you don't rename the folder to remove the "2D" or "3D" prefix, the game creates a new Config file to match the folder name when you first load the mod, but the mod name in that Config file won't match the mod name in the rest of the files. I suspect that's why the mod is loading but not showing up in the game -- the Config file is confused about the name of the mod.
So download the mod again from the link in the first post, choose the 2D or 3D version and unzip it, then rename the folder to "Confederate States of America" by removing the prefix, and put it in your BTS/Mods folder.
It should work just fine.
Happy Holidays!