Yeah, your link goes to the security updates page, but once you click on the Download button, you get taken to an overall updates page. Most of the ones listed for me were billed as security updates, even MS IE 8, which is NOT a security update. Just one more reason why I don't trust Microsoft all that much. I have to wonder what kind of monitoring software they embed in their updates.
I have a flash drive for backing up my data files. I don't have a second hard drive for a fille backup of all apps, and some of them can't be replaced. However, I do keep my anti-virus software current and also have anti-malware software.
That doesn't mean I haven't had a trojan and other malware, even a virus at one point, but at least it all got caught before it damaged anything.
I've seen viruses happen at my old jobs. Amazing, since I'm in IT and IT companies use firewalls and anti-virus software, and almost everyone there knows better - and people still open suspicious emails and download files without checking them.
Sorry to hear your system is requiring all that work. At least it sounds like it's all fixable.