Flash error 16 when using latest Mac version (27.0.0.187) on Safari

Nobody monitoring this forum is an Acrobat expert, but that said, it really seems like the machine is in a bad state.  The things you've tried are totally reasonable, and it hints that something else is probably going on.

As you noted above, it sounds like you had a malware problem.  I tend to agree based on what you're saying here.  I would not assume that the problem is gone just because your machine is no longer exhibiting obvious symptoms.  Malware authors test against anti-malware tools and "cleaners" too, and if they're targeting modern operating systems, they're going to generally be very capable engineers.

At best, whatever happened here left things in a bad state.  The forensic work of figuring out with confidence exactly what happened and how to unroll it is best left to the (very expensive) forensic specialists of the world.  It's generally not worth the time or expense unless you're a defense contractor or something.  It's far easier and cheaper for the layperson to just burn everything down and start over.

If it were me, and I were doing anything remotely sensitive with the machine (banking, healthcare, work, etc.), I'd be seriously thinking about a complete round of formatting the machine and reinstalling the OS and everything else from pristine sources, followed by an afternoon or rotating important passwords and/or adopting a password manager, just in case your keystrokes have been getting logged since you first encountered whatever that malicious payload was that you ran into.

Anyway, the general strategy would be to move your important data to either a USB hard disk or an online file service (Google Drive, Adobe Cloud, etc.) and/or back it up.  Most of the cloud services automatically scan for viruses, so that's a consideration.  Wipe the machine and install a current version of the OS (MacOS lets you boot into a recovery mode now, where it will just download and install the OS with nothing else required -- About macOS Recovery - Apple Support​ ).  Install a current antivirus, reinstall your applications, apply any and all available updates, and then go about restoring your data. 

If you have a ton of data, hopefully you have a time machine backup, and you can just roll back before the original infection occurred.  Since you haven't already done that, I'm guessing it's probably not in the cards.  Because there's a sketchy malware component to this story, I would not simply install over the top of the existing data.  You could, and it might fix the installation symptoms, but the issue if trustworthiness is another matter...

It's also worth pointing out that USB memory sticks can be vectors for malware, and you can infect a USB stick's firmware, such that it will then attempt to install malware on every machine the key is then inserted into.  If you rely heavily on memory sticks and have used one on this machine since the infection, you might think about retiring it with a hammer.  It's cathartic.  (Since your machine is already sketchy, there's no harm in pulling the data off it and putting it on storage that's less likely to re-infect your machine)

Of course, this all comes down to your personal paranoia level and risk tolerance, but identity theft can be expensive and tremendously inconvenient.  Reinstalling your operating system is not an ideal way to spend an afternoon or evening, but it's way better than many of the alternatives.

Sounds like this is a malicious notification, and installer.  Flash Player update notifications don't display that often.  Please post a screenshot of the error dialog (https://forums.adobe.com/docs/DOC-7043#jive_content_id_How_do_I_attach_a_screenshot ). Does it show the link the file is downloaded from?