After battling for another couple of hours with NTRootKit-AC and Generic FakeAlert.a and Generic FakeAlert.d, I decided to give up and reinstall Windows. I moved all my data files to my data partition (E). I wasn't able to access anything external, but I was fairly confident that it would be easy to just clean up my program partitions (C & D).
Well... Things didn't go as well as planned. When I tried to clean up the first two partitions of my disk, for some reason the format procedure thought that the first partition had the full disk size and destroyed all partitions in the process. Including the one with all my data!
So what did I lose, you might ask. Well, besides multiple save games from multiple games I've started and haven't yet finished, including Spore and Fallout 3, and everything that I've added to Quicken since about 6 months ago (when I did the last CD backup) - including all the budgeting that I have been doing in the last couple of weeks, the thing that I'm mostly sad about is that I've lost multiple of my personal projects. That was probably about 80-100 hours of designing and coding. Surely I will take less time to redo it than it took me to go through the first version, but it's just depressing. It's like I'm starting a lot of things from scratch again.
And what doesn't help is that I've already rebooted my computer since I've reinstalled Windows 10 times (and installation took many reboots too because of the mess with the partitions that I've mentioned above). And Windows Update still says that I have 23 updates to install after SP3.
Lesson learned? Maybe quit using Windows? ;-)