winME virus/malware removal

Trying to fix my parents computer. After several attempts I think I have the upper hand. Ran through the house cleaning etc and ran Sas, Spybot (which came to a complete crawl after about 33% scan even though TT was disabled), and finally MGtools. I ran Spybot s&d again and it finally ran the scan in about an hour. Previous to all this I was able to connect to the internet but no access to any web sites. Seems ok now though apart from the startup. Error message " can not find script file c:\windows\temp\net\net.js". This has been happening even before the scans. Also I am unable to perform a manual restore.
I downloaded the supposed fix from MS but doesn't help.
So hopefully when I give them the comp back, Dad will be less inclined to chuck it out in the snow!
Thanks for the help.