I have had difficulty in following your installation instructions. In my opinion, they are poorly worded and imprecise. All instructions should be unambiguous. Please don't assume that anything is obvious. No steps should be omitted.
For example:

Step 4: Add a search form with a query input as shown.
Add the "search form" where? On what page or pages?
Step 5. Add an element to contain the list of search result entries.
Add the "search result" element where? I'm guessing on a NEW HTML page in the root directory, named: search.html
Step 6. Create a Mustache template to display the search results.
Where does this go? In a separate file in _includes folder? or as part of the search.html file?
Step 7. Configure the jQuery plugin for the search input field.
Is this step required or optional?
Step 9. Stop Words
Is this step required or optional?
Step 10. Alternate data directory
Is this step required or optional?