After removal and the reboot as expected the video was messed up but the system was usable so I went to reinstall, starting at 1.0, it came back and said it was there, I looked in Add/Remove Programs and all of the .NET versions were gone, as I would expect from uninstalling them, but no version would go back down.
So I ran my reg checker Registry Defense, I had also run it before the removal and it was clean, this time it said it could not find 87 .dll's, and a ton of other stuff. I tried then to do a system restore, it said it could not restore it.
So at that point I could not remove it or put it back, so I did a disk image restore of HDD 0. The system was exactly as it was before I started. So I tried again, this time after the restart, it again would not let me install, that is when I ran the tool, which I now had, it finished, I rebooted and all the versions from 1.0 - 3.5 went down no issue.
Could have easily been a one-off situation. I keep this machine very clean and rarely run in to any issues, minimal stuff to boot, no "call home programs" (check for updates) except Norton and MS, and on MS updates I do not let them install automatically, Norton Sigs are the only exception to that policy, nothing else is allowed to update without my permission.
I also run TUT from time to time just to make sure nothing has snuck in on me, it just tells you what is running and what it does, what product it is associated with and their opinion on if it should be allowed to run auto, start manual only, or should be disabled, what you do with that info is up to you, it does nothing automatically either. (Like MS Process Monitor on steroids)
In any event, while I was working on I found I was by far not the only guy to have trouble with .NET updates and installs, so I thought I would toss it out there. The experience you have had is my usual experience, things generally go on and off no issue, but when there is an exception it can be a big one, thus my back-up rule...