Drop this like its an old can of spaghetti and get something that would have prevented this from ever happening. Go with ESET Smart Security, I guarantee to you that it would have prevented you from ever accessing the webpage or files that infected the system. It would have quarantined the threat in real time. If it didn't, Malwarebytes Pro (with real-time protection) would have. These two are a lethal combination for online threats, and I am positive you would never have wasted hours of time on this issue.
Btw, before running (/re-running) the above scans that you list, what do I need to turn off?
e.g. On my other (WinXP) computer I am currently running "BitDefender Internet Security", which seems to do about a million different things at once...
Whatever version of BitDefender you have will determine how well it works. Is it the 2013 version? In independent lab results, it got better than it was back in 2009. For some reason, in 2009, it came horrible, and then it came back a few years later, leading on independent results. If this is the paid suite, and its 2013, I'd use it, but I still don't think it would be as effective as the options I listed above. You'd want to thoroughly remove it and restart your computer, prepared already to install the new software.