Its possible that the system is still infected, so it wud be good to get ur HJT examined as per gerry's suggestions. Also you will get advice on ur startup list.
Whats the size of your HD? Is it running full?Maybe theres lots of junk loaded in ur system. How long since you ran a disk cleanup? You can download CCleaner or use the disk cleanup utility and clean out ur temporary files, temp internet files, recycle bin files, etc and then run a chkdsk and after that defragment. This will help speed up things.
For files which u cant delete, have you tried deleting in safe mode?
Also check out this thread in this forum for suggestions to delete stubborn files.http://www.geekstogo...45