Setup.ini has some reference to folders also, if you change userdetails.ini you need to change setup.ini also, otherwise building games will become a problem.
Quote: "The issue that arizes is that FPSC complains when it can't find certain files, and I was curious if anyone knew, specifically, what these files were."
I've had the same problem as well. Here's how I solved it.
1. Copy your original modified FPSC to a different folder
2. Repair FPSC.
3. Move the repaired version to a different location.
4. Copy your original modified FPSC back.
5. Now start moving missing files from the repaired version to the modified version.
You could also install a second version of FPSC and move files around, but that may cause uninstall problems. The way I did it only creates one uninstall file.