all of your graphs look OK, I'm fairly sure (with 99% certainty) that your site isn't penalized....
this could become problematic and tank your site, you need to be careful with what you're doing...
1) use a tool like Screaming Frog (or any other site auditing tool that you can afford as you'll probably need a paid tool for this) to audit your site and find all technical issues of your site (404 pages, broken links, useless / looping redirects, missing tags, etc... anything that the tool finds note down with the intention of fixing before or after you overhaul the site, depending on what's needed when)
2) note down the best performing pages of your site (the ones that rank the best, the ones that are targeting the toughest keywords and are still ranking decently, the ones bringing you the most traffic / revenue, or any combination of these 3 criteria) and save their exact URLs, as well as any internal links pointing to these pages (that's where a site auditing tool like Screaming Frog can be so useful, because it shows all internal links pointing to all of your pages)....
When you have these important pages (and the internal links) written down, fix these pages first and if you intend to keep their URLs intact (which I recommend) you can then fix any internal links that might be broken / missing that are pointing to these important pages... or - if you intend to change the URLs of these important pages - make the necessary on-page SEO modifications first and then, after you update the changes and the URL changes, 301 the old URL to the new one, and then make the internal links that were pointing to the old URL point to the new URL instead (the one that you used as destination in the 301 redirecting box)
Most likely, there will be more things you can do, but you'll know them after you run a site audit first, as the audit will mark all of the things that are wrong with your site.
But, as a general rule, when updating / improving pages that are already ranking the most important thing to pay attention to is the change of URL and site structure. If the URL of any of the important pages changes you need to immediately 301 redirect the old URL to the new one before re-submitting the sitemap to GSC and / or before google re-crawls the old URLs and find 404 page (due to URL change) and thus remove your page from the SERPs.
