Wow, good job.. Wouldn't it all be easier with a fresh install? Too late for that, so nevermind.
First you could've tried following this
guide, but the computer is workable already. You can still use some of the tools within it though.
Anyways, you can try more scanners (Avira recommended), but I'd try to fix more problems first by using Advanced System Care (or another all-in-one, or separate utilities). Also you can try some rootkit removers like Panda Anti-rootkit, etc.
Well, good luck using the computer.