I was new to WordPress a few weeks ago, and had already created a site using Javascript includes for the footer, sidebars, and footer and CSS for formatting.
For using them with WordPress, I changed all the links to complete URLs instead of relative URLs.
I created my own theme for WordPress by copying the regular site’s index page for the WordPress index page. I left the header and footer includes, but replaced the sidebar include with a call for WP’s sidebar.
I did not use the style.css file in the WP template folder (except to define the template) and instead left the call to the main site’s stylesheet.
Then, of course, I took out the “main” part of the original index page and inserted “the WP loop.”
I started the WP sidebar file by copying the original sidebar include, then added desired WP features, such as search, categories, and login to the sidebar file.
After I got all that done, I created a “single” page similar to the index page.
I use “if” conditionals to determine the heading text on the index page (e.g., if it’s a category or archive page).