A lot of the mods are available only through the catalogue and shipping station. There is a shelf in Leif's store that will rotate some of the items from the mods through. But if you installed a bunch of mods it will take a long time for the items to rotate through. I know that one of the mods uses the bookshelves in Aliza's store, the ones behind the cash register. That mod is Auto-Magic I think.
You might try clicking on the play button in your library for your game. Choose Run Mod Manager. Once the mod manager is open, there is an option in Tools for Run Content Builder. Run that and then open up the game again.