There was a firmware update last week and I tried it thinking that it couldn't make the phone any worse. After the update malwarebytes no longer flags the settings app, but I did notice an odd blank notification from an app called essqz, which I had never seen before. It could have been installed already, but if so I never noticed it when going through the apps lists over and over the past few months trying to clear out malware. It certainly never gave a notification before... a google search didn't turn up any results for it.
I also seem to be unable to update any apps in the google play store; they get stuck at "pending" and never go forward from there. Again, only since the firmware update.
To reiterate, I've had luck avoiding pretty much all of the popups and malware after resetting my phone and keeping wifi completely off, so from that last reset up until now I still hadn't seen anything suspicious. I'm not sure if anyone else has gotten the update and noticed anything different