Hi everyone,
I just wanted to post a quick follow-up. Modifying ownerships and permissions on files and folders, even resetting all permissions back to Windows defaults, didn't resolve my problems, but I was able to figure out the underlying cause (still haven't "fixed" that cause, and probably won't try to, given its nature). Also, running SFC didn't reveal any problems that could be fixed by the SFC automatic processes.
The reason why certain programs, including ReShade, refused to work was due to corruption of my Windows user identity profile. This became the most likely possibility when even a "clean boot" didn't resolve the issues but running a different user worked fine (Administrator in the first case, and then a new profile afterward). This was also the cause of ESO crashing after ReShade loaded its first shader. I started a new, clean user account and everything works perfectly fine. So although my user profile doesn't work and I have to migrate everything to my new one, at least on the new one, ESO with ReShade is working great.
So for anyone else who comes across similar issues in the future, try a different user profile on your computer, even if you have to create a new one, and see if things work ok there. If it does work in a clean user profile, but not on a "clean boot" to your normal profile, then it is a problem with your user profile.
I hope that helps someone in the future to have less frustration if they ever come across this particular problem, but I also hope no one else ever has to deal with this problem.
Later,
Drake