Yoast SEO Plugin not recognising content from the Wordpress Template
Solution 1: 
Yoast SEO can only give you a score based on DB content that it can read. That being said, just because Yoast SEO can't see your content doesn't mean that search engines can't. Unfortunately, unless you get your content out of the template and into WordPress, your Yoast score will never improve.
I'd recommend (if possible) to try to get that content into WordPress. It's just not best practice to hard-code content into template files. Consider using Custom Fields if you have specialized content that won't work in the WYSIWYG.