to explain what happened, most likely (i have made a few of these in my time.. l0l)
the spyware infected your registry and corrupted IE, try reisntalling IE after cleaning up after the spyware, and spyware remover (the spyware remover will have done its job and removed the infected registry entries and files that resemble spyware.. or they simply took a chunk out of IE that it has been made to rely on) clean up...(this is why sometimes reformat is used instead, it depends on how fucked yup your registry gets... and your OS etc... and whether you will spend the time to clean it up...)
Also do check what is in your startup folder take things out and see if that helps!
Also to check the hardware side of the issue do you have enough ram etc?? please list your stats, this is probably not the problem, but best to check all possiblilities when messing with computers...
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