So, solution update. Editing the files via the webconfigurator was my problem. It seems as though the editor was saving blank files instead of my changes, and as such nothing was working. I edited the files with VI and the cert was accepted into the system. I do still have a issue with a different upstream cert, but I can fix that based on my fix with this one.
Thanks for everyone's help, I'll try to add a guide on my site for this because I couldn't find anywhere online that referenced both files.