Adding Custom JavaScript, CSS And HTML To WordPress

I have a simple code that counts number of words in a sentence. This word counter has 3 parts, a CSS, JS & HTML files. I know its possible to run this scripts in WordPress but

Solution 1:

JS and CSS
There are multiple ways. I would start reading this. As you mentioned wp_enqueue_script is a good way:
http://code.tutsplus.com/articles/the-ins-and-outs-of-the-enqueue-script-for-wordpress-themes-and-plugins--wp-22509

HTML
You're looking for Child Theme:
WP:A WordPress child theme is a theme that inherits the functionality of another theme, called the parent theme. Child themes allow you to modify, or add to the functionality of that parent theme. A child theme is the safest and easiest way to modify an existing theme, whether you want to make a few tiny changes or extensive changes. Instead of modifying the theme files directly, you can create a child theme and override within.