The index files have to be placed inside the theme folder. The only files that you need to place inside the theme-custom folder are the style sheets and images.
P.S.:
We are currently renewing our tutorials. The structure has changed since Mendix version 2.5.1-RC1 (login page is different, imports are gone, base files are gone). We hope to have the tutorials online by next week!
I've made several themes for 2.5 and struggled also with creating the package. Why do you want to use the theme switcher? Try this:
Start your project with this zip, this should work. Is there some reason why you want to use the theme switcher?