Ok, so I figured out what the problem was.
I had mistakenly thought that I edited the missionscripting.lua file because when I opened it up in notepad++, it looked right. Turns out that the way it was set up, I was just looking at a version of the file that I had edited but not saved.
Trying to edit the file gave me access errors, so even when I did it successfully using administrator privileges, saving the campaign in game didn't work because there weren't sufficient privileges to write the MDC_campaign_results.lua file.
Thanks for taking the time to try to help me troubleshoot the issue, MBot. I also wanted to state what many others have said that this is a freaking amazing mission, thank you for creating it for us to play.