I don't know if this is the place for it, but I just want to thank whoever accepted this submission. It was about a day of work to manually put the facial expressions on each portrait, along a few other things I had to work too.

For anyone's curious, I didn't understand Godot's Engine programming for how the facial expressions were being handled (the engine this game uses). Not knowing the values, I resorted in going into the game's story mode, and taking screenshots on the game's native resolution for most of the dialogue that happens.

With the screenshots, I would add a temporary layer on Paint.NET with the "Difference" mode. This way, I could put the facial expression image exactly at the right spot. Placing the screenshot I took above the extracted portrait file from the game files at the correct placement would make the image completely black (which means there was no difference), with the exception of the facial expression of course, due to the portrait's file having it blank.

To fix the facial expression being different, a layer in the middle of these two was made to add the facial expression image. Placing the facial expression manually at the right spot left the portrait without a single difference from the game's screenshot and extracted files.

Then it was a simple case of deleting the top layer (the screenshot I took from the game's window), and merging the facial expression layer with the portrait. And that's how I managed to get the facial expressions at the right spot without knowing the game's programming language.