Before rewriting the article, roll out a new server. Seriously. It seems you do not have the skills yet to do a proper audit. It’s better to roll out a pristine server. If that is a lot of work, it is a good moment to learn about declarative system configuration.
At any rate, this happening to you sucks! Hugs from a fellow HN user, I know that things like this can suck up a lot of time and energy. It’s courageous to write about such an incident incident, I think it’s useful to a lot of other people too, kudos!