Next I came here and after trying a few of Keith's suggestions was sent back to Malware's 3-day-no-response forum.
Finally got some help on Malware, tried several more things, ended up with Armodeluxe saying,
"I can't comment on the defragmenting issue as it is completely beyond my knowledge..I suggest that you make a post on Windows forums (tell them that you got a clean bill from Malware Removal) and the staff there would be able to help you on that issue hopefully..
Here is the Malware log of what has occured so far:
Basically, I can't open up "My Computer" from the start menu, I am getting inundated with pop-ups, and most importantly when I run XP degragment - none of the (tons of) fragmented files get moved.
So, if there is anyone who can fix this it would be most appreciated.