I had similar issues to everyone. Here's the fix:
Put the 'Mods' folder (Data > Mods) inside the 'patch' folder of your Pokemon Rejuvenation game.
Now put the 'Followers' folder (Graphics > Characters > Followers) inside the 'Characters' folder of your your Pokemon Rejuvenation game (Graphics > Characters).
The reason why Pokémon followers appear as a question mark graphic is because the mod is specifically looking for a folder with sprites within the game's base 'Characters' folder, not inside of the patch folder.
Hope this helps!