Here's a current update:
I made a Hiren's BootCD and I'm using it to back up a lot of data just in case I can't get all of the malware off, but so far I've found a lot of it and removed it.
I've located the trojan lurking in my Windows/Installer folder as well as in the AppData/Local folder and removed it.
I've deleted various adware/spyware and tracking cookies.
I've run a checkdisk using the BootCD, and I'm still going to do a scannow when I'm done copying everything.
If you're in a similar situation and either can't boot into Windows, or Windows keeps kicking you out, I would highly recommend the Hiren's BootCD. It's got most tools you need to recover data and remove stuff without having to get into Windows first. You can also use it to edit the registry. Download Hiren
Why? It's like killing roaches. They won't go away. Whatever you learn about virii and Win internals will be useless soon enough, as that all changes quickly.
This is assuming you're not planning on doing this as a "profession."
I suggest you keep a clean house with a recommended anti-virus. A free one.
Paying for an anti-virus just supports the "virus "industry."
Maybe even more important, take image copies. Then the roaches are inconsequential. If I even suspect roaches, I just replace the house with a clean one. 5 minutes.
I get where you're coming from, and used to have "fun" squashing roaches.
After a while it became distasteful - like, do roaches deserve much of my attention?
I like to learn, I like to work on the computer, and I like to develop new skills. I don't consider that at all a bad thing.
This is also the first time in maybe eight years that I've had a virus.