CA Updated M2 and pushed a large update to include multiplayer support for M2 today. You may notice if you are a Steam user that Kingdoms is no longer a separate entry in your library. It is now shown as a DLC for M2. They have also disabled the launcher in favor of a launcher to select campaigns directly from Steam.
YOUR MODS ARE FINE.
And you will be able to play TATW
You just must rename your Third Age Total War folder to one of the existing campaigns such as americas then select that campaign from the new Steam launcher.
Posting as I hadn't seen a solution posted yet and I am sure others wont come across the solution so quickly.