Hi,
The Menu Framework doesn't have some of those features (since it's really intended to just be a starting point), but we'll get through as many as we can. Let's take each one step by step, starting with the save system.
I recommend these steps:
1. Add an instance of the Menu System prefab to a new, empty scene. Then drag the Menu System from the Hierarchy view back into the Project view, in one of your own folders. Unity will ask if you want to "Create Prefab or Variant?" Click Create Prefab Variant. By creating a prefab variant, you can customize the appearance and settings of the variant without worrying about losing your customizations if you ever import an updated version of the Menu Framework package.
2. Then open your own main menu scene. Add your Menu System prefab variant. (Remove the previous Menu System GameObject if the scene has it, so that there's only one.)
3. Add Dialogue Manager, Quest Machine, and Love/Hate Faction Manager GameObjects to the scene. None of these GameObjects should have a Save System component.
4. Download the Save System Prefabs package (
direct download) from the Extras page. Import the package. Then add the Save System prefab to the scene. This prefab is preconfigured with the save system components and scene transition manager.
5. Add your main menu scene and the LoadingScreen scene to Unity's build settings. Also add at least one gameplay scene. You can add more gameplay scenes later.
6. Inspect your Menu System prefab variant in the Project view, and locate the Save Helper component. Set the First Gameplay Scene field to the name of the first gameplay scene in build settings. If you've added a credits scene to the build settings (see the Example folder's Credits scene), locate the Title Menu component and set the Credits Scene Index to the build settings index of the credits scene.
Give that a try. Make sure you can start in the main menu scene, start a new game, do some stuff, and save the game. Then return to the main menu and make sure you can continue or load your saved game.
Once you know that works, you can add an instance of the Menu System prefab variant to your gameplay scene(s). Expand this Menu System in the Hierarchy view, and deactivate the TitleMenuPanel child GameObject. This will let you start play mode from the gameplay scene instead of the main menu scene if you want, for quicker playtesting.
Once you've confirmed that this all works, we can look at the other items.