have you tried using an online scan?
http://antivirus.trendmicro.com ?
otherwise, you could used the "ultimate boot cd" - it has antivirus on it...
http://ubcd.sourceforge.net/
as for your ie.cache problem-- have you tried to rename the file(s) before deleting them? or shift-delete?
oh, and your popup problem -- are you running XP? is the messenger service disabled?