My website is not WordPress or any other pre made script. It's completely custom. I spent 6 months making it in my spare time and it totals well beyond the size of WordPress in terms of code base. Another reason why it's so unfortunate. It's had a couple of rip-off's but they don't even really rank. One was even a scraper, but I blocked it many months ago so it doesn't appear to be the causer of any issues.
I'd love for some SEO style blog or agency to do a case study on my site like you suggested. But in all honesty, I'd love to just know why the site is penalized.