I have full access to the system. I designed the database and wrote the search function and the ft_stopword_file is not set there. It's a global MySQL variable.
Basic information on the variable can be found in the MySQL Manual section 12.7.4 Fine-Tuning MySQL Full-Text Search. This section says the actual ft_stopword_file variable will either be set to a file path (which would be great!) or direct MySQL to an interal list, mine is directing to an internal list.
I know I can create a new file, change the variable to the new file path, and rebuild my index. But I wouldn't know what words I'm missing in my new list. So I guess my biggest concern at this point is seeing the current stopword list, which is now an internal part of MySQL...?