No, I actually tried that--putting the (copied) SNT files and (custom) OGG files into custom_stories/[nameofcustomstory]/sounds, then opening the copied SNT file with Notepad/Notepad++ and changing the sound names to those of my custom OGG files. But when I try going back into the game and opening my custom story, it still plays the original files.
I searched the forums before posting, but all I could find was this thread, which is for changing the sounds for all custom stories/the game itself:
http://www.frictionalgames.com/forum/thread-6060.html
Here's my edited SNT file (the one in my custom story's sounds folder):
<SOUNDENTITY>
<SOUNDS>
<Main>
<Sound File="newhurt_pant1" />
</Main>
</SOUNDS>
<PROPERTIES Volume="0.5" MinDistance="1" MaxDistance="10" Random="1" Interval="0" FadeEnd="False" FadeStart="False" Stream="False" Loop="False" Use3D="True" Blockable="True" BlockVolumeMul="0.5" Priority="0" />
</SOUNDENTITY>