I know of only two instances where I've ever definitely been infected with spyware. I don't do stupid things like downloading and running strange programs from third-party sites, so I think both infections were probably caused by a site exploiting a security hole in Internet Explorer, or in a plug-in like Adobe Acrobat or the Flash player. Both times, once I noticed I was infected, I got rid of the infection with Malwarebytes, but I don't know how much damage the spyware did in the meantime.
Malwarebytes is good software, but as you point out you don't know how much damage was done. Secondary infections can easily be missed, and many malware programs open your machine to further exploitation. As tired as the suggestion is, you needed to do what you did with your website: revert the machine to a known good backup of the system state, formatting first. Anything less and you *should* have that nagging doubt that you haven't actually cleaned everything up. There are ways to diminish the concern: inspecting the machine for unexpected packet flows, using anti-rootkit tool, etc... but only by formatting and restoring a know clean state or formatting and just restoring your data files will you be confident).
"That's the second thing that's wrong with it. It punishes success."
How right you are. We should return to the model where the failures pay for everything. Just rename the poor as peasants, set the various city, county, state and federal tax collectors up with cool names like the Baron, Duke and Lord and we will have returned to a classic system that didn't punish success.
Of course if that is too extreme, you could always try to be successful in a failed state. I hear that openings for local warlord are surprisingly common.
Where do I get all these magical digital freedoms? You make it sound like the Broadcast Flag and DMCA magically vanish with over the air transmission, and the content providers are going to sing Kumbaya with us as we rip their content in the ways we want to.
I have my doubts.
Kleeneness is next to Godelness.