Pre-Preamble
This assumes some experience with godot at the level of replacing materials/other resources inside nodes (I should be attaching pictures for reference regardless), and is more of a connecting the dots explainer. While technically possible to do otherwise, I'm going to say that all of this requires working in Godot in a decompiled project of the game.
Being comfortable with the command line is borderline necessary as you get further into this—again, not necessary, but it makes automating the pain points of all of this much easier.
Preamble
Some background on the details/pitfalls of loading mod content, I apologize but its important—these are all things I which I fully cemented in my brain earlier, for now just keep them in mind as we go through the actual details.