Hi there.
Well, here is a bummer for you - metrics don't matter. If we were in perfect world, yes, the websites with higher metric scores would be ranking higher, but it's not true at all. There are so many factors Google is including in their algorithms, and nobody knows what those are.
Instead of looking at metrics, look at actual content, on-page optimization. What about technical SEO? Also some of your backlinks have high spam score - that might be hurting.
As for penalilzation - if you were penalized, you for sure wouldn't be #4 - you'd be number #104 if ranked at all. Check your Google Search console for manual actions, if there are none, then you are not penalized, you just need to work harder on your SEO. Which area you ask - nobody really can give you better answer than yourself. You know your website best and you know which areas are the weakest (on subconscious level for sure).
Hope this helps.