Sorry, it is Catalog --> Products With Attributes. It's most definitely Stock By Attributes.

When I uploaded the files, I uploaded the includes and admin files straight to the root directory (unless I mis-read, that's what the readme says to do to install the mod), so I'm not sure how they would have gotten in the wrong place.

Where is the extra box file so I can check it?

Sorry if these questions are way basic/vague. I'm new to this program. I really appreciate the help though!