was the modfolders exe inside the Mods folder or in the same folder as sdt and loader? It should be in the Mods folder.
you can create your own characterfolders.txt file with notepad, and just list, one entry per line
Name To Show In Loader:name_of_folderWithCapitals and probably spaces
here's a couple of mine:
A Pair of Damsels:pair_of_damsels
Camp BJ:CampC-BJ
Maid Fun:5_girls_floral
(the last one was a project that changed courses partway through and I renamed it in the list instead of changing the folder name)
Putting the position files in settings is where they go by default, though the later animtools and dialogactions (forget which) can pull them from elsewhere as well. (typically the same folder as the animtools.swf is, either the character folder or INIT)
If nothing else works, I'd just open the zip you downloaded for the loader, and extract the loader and sdf swfs again.... just in case something modified them that shouldn't have.