Windows Going To Shut Down Pop Up At The Start Up

My Uncle just got a Dell computer and installed a dsl modem, and after a couple of days the computer was running super slow, and a popup appeared a few minutes after startup with a 60 second timer saying that windows was going to shut down. I thought that it was Spyware/adware so I installed and ran Adaware, and I deleted over 380 infected files, and ran AVG 7 virus scan and detected trojan viruses. I saw that his internet security settings were set at the minimum level and the firewall was disabled, so I enabled the firewall and raised the bars on the security levels, but there's still a major problem.