Everytime I try to open themevars.rc, I get a message saying, "A previous instance os LiteStep was detected. Are you sure you want to continue?" After clicking yes, I immediately get a message saying "You are currently running another shell. While LiteStep b24 allows you to run under Explorer, we don't advise it for inexperienced users, and we will not support it, so do so at your own risk." Explorer is not loaded or even in the task manager, so how else can I open the file to customize the theme?

Have you tried 'rightclick > open with...' ?

And don't associate your rc files with litestep.exe. They're just text files. :P

and update your litestep build to 0.24.7 final.

Or even one of the newer dev builds.