It seems that when I was doing the back-up of the site the /mods directory got somehow left out. I've since reuploaded everything and they should be in working order. If you find that something doesn't work, please reply to this post with the details. *note: This fix does not apply to the forum attachments that don't work. Something messed up with the back-up system that left those files corrupted. They will need to be reuploaded. Just e-mail them to me and I'll put them up on the FTP permanently.
While this doesn't really address the issue of how to replace the original files, I'll point out that the levelup_mod.zip that zhuge posted in the "make your npc's level like pc's" thread in general mods still downloads complete and works just fine.