OK, I've come up with a stopgap solution. I'll just install FS2 on another computer, move the missions over with a flash drive and set up the campaign linking on that one. Hell, that'll have the pleasant side-effect of having my mission and campaign info in three different places (PC number 1, PC number 2, and USB drive) in case of a catastrophic hard-disk failure.
EDIT: OK, found a massively less inconvenient solution. Just use the default non-SCP FRED2. I can't think of any reason why using a non-SCP campaign editor would be TOO much of an issue.
ANOTHER EDIT: Alright... after some troubleshooting, it seems that I've somehow fsked up my FS2 game directory in ways I cannot even comprehend. Screw it, I'm just gonna reinstall.