This is the only question I see, so let’s try to answer it.
First of all, always link to the full site repo, so we can clone and run the site ourselves. We can’t troubleshoot without seeing a lot of different templates. Refer to Requesting Help for more guidelines.
What is the URL you are trying to get? Something like example.com/handbook/manuals? What shows on that page? Is it a single content file, or a list of other content?
Share your site’s source code, it may make more sense. 
Also, please change the title of this title to be something relevant. Your issue isn’t a “404 page not found”, it is about template lookup order and creating sections and lists.