After much discussion won permission to put the affected machne back on the internet, in order to update the virus definitions. Followed all of the intructions as given, but widows defender was unable to update... (error code something, no more info given) so i did a manual update, and that seemed to work fine.
The kaspersky scan found 220 infected files, all but about 25 of them were in system restore, so I flushed it as described in step 1. All but one of the remainder were in Qoobox quarantine (combobox?), when I ran avg it picked them all up, but when I clicked apply to all, the save report button greyed out, even though I'd followed all the other instructions fine, so I dont have the avg report. So, timeline goes:
Sdfix (report attached)
Kav online scanner (report attached)
Flushed system restore
ATF cleaner
AVG (but no report)
HJT (report attached)
(I had to convert the kavscan to .txt, so formatting may be wonky, also, scan interrupted by user was because it got stuck scanning a disk accidentally left in the drive.)


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