For malware 2-squared is the best scanner currently, its not as good picking up adware and spyware but really good at finding trojens/ and downloaders for botnets. Also they have a better "Highjackthis" Utility you may like using.
I would run Rootkitrevealer as well... go to the forums to look up the results u get
Also scan in safe mode or the cleaning process of these spyware cleaner utilities is mute.
I am really surprised that you have not just reformated the machine. ESP a windows 2000 box. Once infected malware you are SOL as far as making sure that you missed something.... A pc reinstall takes 3 hours tops, I'm sure you've wasted a lot more time than that already... Also you have a VB problem on top of it..... Isn't your time worth money?