matt-u

you've probably done it, run a disk cleanup to remove the junk and checked the disk for errors? What about checking ur fragmentation levels, as these could be a reason for slowdown.You could also maybe clean out the dust from the cases and check if all your fans are working fine. Its possible ur system is still infected, maybe you could get ur log checked by a HJT expert. Also try unwanted items from startup,see if it helps.

Check out this link, http://www.computerhope.com/issues/ch000646.htm I guess if your HD is severely fragmentation of HDD may also a reason for this problem ,probably some key files needed for booting were badly fragmented.