When doing a custom story, you are forced to use all default settings for the player and you can only change the levels and add new assets. If you want to change stuff like player speed, sanity properties, menu style and the like, you need to do a full conversion.
The most important file for this is the “config/main_init.cfg” file. Make a copy of this file and name it something like “main_init_my_mod.cfg” and place it somewhere. Preferrably would be to place it inside a new directory in the install root, for example “my_mod” (make sure to not be too generic in names so there will be no name clashes later on). Note that you can NOT have spaces in the name! Now place all of your updated config files in the “my_mod” folder and simply link to them in the main init.
To start your full conversion either make a program shortcut or a batch file like this:
This will make the game load your custom init file instead of the default one.
See the page for main_init.cfg to see what the properties do.