So my roommate managed to get a virus last week, and asked me to clear it for him. While I usually just tell him to save important data and reformat / reinstall, he said he had JUST started to see signs he might have picked something up, so I figured I'd humor him.

The virus appeared to just be emulating a Windows looking security type program (Warning you have 99 pieces of malware on your computer! etc), and was trying to install tons of more stuff, spamming the windows "give access to this program" security warning. Thinking that I might have caught it early enough, I booted safe-mode and ran MSE and cleaned it up. Program history showed it as a Trojan downloader called Exdoer, which had downloaded a few others: Renos.MJ, Hiloti, VB.AGA, Meredrop, and Fakerean. Which is actually kind of impressive considering it was only compromised for a few minutes, if the logs are to be trusted.

Anyhow, everything looked clear according to every scan I could run, and his computer went back to normal, until about 3 days later. He's now getting hangups on just about every program running at random intervals, for around 20 seconds to 1 minute. Normally at this point I tell him to nuke it, but the lag is the *only* thing wrong with his system as far as I can tell. All scans hardware and software are fine, and there isn't even any anomalies in the outgoing wireless.

Are there any diagnostics that I might have overlooked that can tell me whats going on?
And in the event of a reformat, could media from the old system be trusted to be ported over?

Thanks.