There are some bugs with modding certain files. The only way to be sure is to backup the files in the game folder and then replace them with your modded ones. No need to quit playing. 

Thanks for the replies. A little sleep cured most of my frustration. I guess overwriting the original files is the easiest solution, although I had been trying to avoid doing so. I originally started out that way, but hoped to take advantage of the mod folder.

I would bet dollars to cents that these mod bugs will be fixed. The devs just haven't started that kind of prioritizing. We are at least on their radar now.