user_keys.cfg

[Romulator]

To make the Crouch Button Left Alt, just do it yourself in Amnesia's in-game settings from the Main Menu. There is a Controls tab where you should be able to assign Left Alt as your preferred Crouch key.

If you need to make this the default for others when exporting your Custom Story, you will need to make a Full Conversion mod, and include the default_user_keys.cfg file with your story, and modify files accordingly. I believe the main_init.cfg has a setting you would need to change.