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A custom story takes advantage of Amnesia's in-built Custom Story menu option in the main menu. It is much more easily developed, maintained and installed and is generally just copy+paste and you're good to go. However, doing so tends to impose constraints on the developer should they need to access specific options, as some can affect the overall impression the Custom Story requires.
Full Conversions take advantage of using a 'seperate' Amnesia game, not linked to the actual main game itself. Doing so, creativity is much more accessible, being able to do things such as changing the lantern, modifying Daniel's height, running/walking speeds, determine how low the light setting can be before sanity effects appear, among other things. Full conversions, depending on the way they are set out, can be a nuisance to install, as some have differing instructions on doing so and can be a pain in the neck sometimes to set up as a developer. They do have the advantage of being able to provide the player with a somewhat more appreciative and different approach with was required by The Dark Descent, but unless these advantages are fully exploited, communicated and demonstrated, a Custom Story project is probably much better.
In simple terms:
- Custom Story: Limited functionality by Amnesia: The Dark Descent's options, however easy to install and set up.
- Full conversion: More functionality, yet difficult to maintain and can be a nuisance to install.