I recreated my site recently and moved the custom PHP and WordPress code to a central WordPress code base. I had to recreate some files in the template to get the site to behave the way I wanted it. This is the list of changed files in a WordPress template.

404.php
comments.php
content-page.php
footer.php
header.php
index.php
page.php
sidebar.php
single.php

Of course you’ll have to add the style.css file and include custom Javascript and CSS files in your header.php file.